diff --git a/.chloggen/crds_wip.yaml b/.chloggen/crds_wip.yaml
new file mode 100644
index 0000000000..7145465f4a
--- /dev/null
+++ b/.chloggen/crds_wip.yaml
@@ -0,0 +1,16 @@
+# One of 'breaking', 'deprecation', 'new_component', 'enhancement', 'bug_fix'
+change_type: enhancement
+
+# The name of the component, or a single word describing the area of concern, (e.g. collector, target allocator, auto-instrumentation, opamp, github action)
+component: webhook
+
+# A brief description of the change. Surround your text with quotes ("") if it needs to start with a backtick (`).
+note: Allow to run the mutating webhook using static configuration, without the need for CRDs.
+
+# One or more tracking issues related to the change
+issues: [4201]
+
+# (Optional) One or more lines of additional information to render under the primary note.
+# These lines will be padded with 2 spaces and then inserted directly into the document.
+# Use pipe (|) for multiline entries.
+subtext:
diff --git a/.github/workflows/integration-test.yaml b/.github/workflows/integration-test.yaml
new file mode 100644
index 0000000000..65f052252d
--- /dev/null
+++ b/.github/workflows/integration-test.yaml
@@ -0,0 +1,49 @@
+name: CI
+on:
+  push:
+    branches:
+      - main
+  pull_request:
+jobs:
+  java-autoinstrumentation:
+    env:
+      KUBECONFIG: /tmp/kube-config
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - name: make our image
+        run: VERSION=dev make container
+      - name: make java autoinstrumentation image
+        run: |
+          cd autoinstrumentation/java && docker build -t java-autoinstrumentation:dev --build-arg version=$(cat version.txt) .
+      - name: Create kind cluster
+        uses: helm/kind-action@v1.11.0
+        with:
+          cluster_name: kind
+          node_image: kindest/node:v1.27.3
+      - name: Deploy certificate signing request
+        run: kubectl apply -f tests/integration/certs.yaml
+      - name: Approve our certificate signing request
+        run: kubectl certificate approve operator
+      - name: register our image
+        run: |
+          img=$(docker images | grep operator | awk '{print $1":"$2}')
+          docker tag $img manager:dev
+          kind load docker-image manager:dev --name kind
+          kind load docker-image java-autoinstrumentation:dev --name kind
+      - name: Deploy collector
+        run: kubectl apply -f tests/integration/collector.yaml
+      - name: Deploy operator
+        run: kubectl apply -f tests/integration/operator.yaml
+      - name: Sleep 10s
+        run: sleep 10
+      - name: Deploy java app
+        run: kubectl apply -f tests/integration/java.yaml
+      - name: Sleep 20s
+        run: sleep 20
+      - name: Check logs
+        run: |
+          COLLECTOR_POD=$(kubectl get pod -l app=collector -o jsonpath="{.items[0].metadata.name}")
+          LOGS=$(kubectl logs ${COLLECTOR_POD})
+          echo ${LOGS}
+          echo ${LOGS} | grep "Starting Servlet engine"
\ No newline at end of file
diff --git a/internal/config/config.go b/internal/config/config.go
index cd874232f4..c11a07014e 100644
--- a/internal/config/config.go
+++ b/internal/config/config.go
@@ -121,6 +121,21 @@ type Config struct {
 	Zap ZapConfig `yaml:"zap"`
 	// EnableWebhooks enables the webhooks used by controllers.
 	EnableWebhooks bool `yaml:"enable-webhooks"`
+	// Instrumentation is the set of instrumentations to use if CRDs are not present
+	Instrumentation Instrumentation `yaml:"instrumentations"`
+	// EnableInstrumentationCRDs enables looking for instrumentation CRDs.
+	EnableInstrumentationCRDs bool `yaml:"enable-instrumentation-crds"`
+}
+
+type Instrumentation struct {
+	ApacheHttpd *InstrumentationSpec `yaml:"apache-httpd,omitempty"`
+	DotNet      *InstrumentationSpec `yaml:"dotnet,omitempty"`
+	Java        *InstrumentationSpec `yaml:"java,omitempty"`
+	Go          *InstrumentationSpec `yaml:"go,omitempty"`
+	NodeJS      *InstrumentationSpec `yaml:"nodejs,omitempty"`
+	Python      *InstrumentationSpec `yaml:"python,omitempty"`
+	Nginx       *InstrumentationSpec `yaml:"nginx,omitempty"`
+	Sdk         *InstrumentationSpec `yaml:"sdk,omitempty"`
 }
 
 // New constructs a new configuration.
@@ -172,7 +187,8 @@ func New() Config {
 			LevelKey:    "level",
 			LevelFormat: "uppercase",
 		},
-		EnableWebhooks: true,
+		EnableWebhooks:            true,
+		EnableInstrumentationCRDs: true,
 	}
 }
 
diff --git a/internal/config/config_test.go b/internal/config/config_test.go
index 6c542fe162..5b1fb3a1cf 100644
--- a/internal/config/config_test.go
+++ b/internal/config/config_test.go
@@ -36,6 +36,7 @@ func TestToStringMap(t *testing.T) {
 		"enable-apache-httpd-instrumentation":     "false",
 		"enable-cr-metrics":                       "false",
 		"enable-dot-net-auto-instrumentation":     "false",
+		"enable-instrumentation-crds":             "false",
 		"enable-go-auto-instrumentation":          "false",
 		"enable-java-auto-instrumentation":        "false",
 		"enable-leader-election":                  "false",
diff --git a/internal/config/instrumentation.go b/internal/config/instrumentation.go
new file mode 100644
index 0000000000..c3f2b4da92
--- /dev/null
+++ b/internal/config/instrumentation.go
@@ -0,0 +1,412 @@
+// Copyright The OpenTelemetry Authors
+// SPDX-License-Identifier: Apache-2.0
+
+package config
+
+import (
+	corev1 "k8s.io/api/core/v1"
+	"k8s.io/apimachinery/pkg/api/resource"
+)
+
+type (
+	Propagator string
+)
+
+const (
+	// TraceContext represents W3C Trace Context.
+	TraceContext Propagator = "tracecontext"
+	// Baggage represents W3C Baggage.
+	Baggage Propagator = "baggage"
+	// B3 represents B3 Single.
+	B3 Propagator = "b3"
+	// B3Multi represents B3 Multi.
+	B3Multi Propagator = "b3multi"
+	// Jaeger represents Jaeger.
+	Jaeger Propagator = "jaeger"
+	// XRay represents AWS X-Ray.
+	XRay Propagator = "xray"
+	// OTTrace represents OT Trace.
+	OTTrace Propagator = "ottrace"
+	// None represents automatically configured propagator.
+	None Propagator = "none"
+)
+
+// InstrumentationSpec defines the desired state of OpenTelemetry SDK and instrumentation.
+type InstrumentationSpec struct {
+	// Exporter defines exporter configuration.
+	// +optional
+	Exporter `yaml:"exporter,omitempty"`
+
+	// Resource defines the configuration for the resource attributes, as defined by the OpenTelemetry specification.
+	// +optional
+	Resource Resource `yaml:"resource,omitempty"`
+
+	// Propagators defines inter-process context propagation configuration.
+	// Values in this list will be set in the OTEL_PROPAGATORS env var.
+	// Enum=tracecontext;baggage;b3;b3multi;jaeger;xray;ottrace;none
+	// +optional
+	Propagators []Propagator `yaml:"propagators,omitempty"`
+
+	// Sampler defines sampling configuration.
+	// +optional
+	Sampler Sampler `yaml:"sampler,omitempty"`
+
+	// Defaults defines default values for the instrumentation.
+	Defaults Defaults `yaml:"defaults,omitempty"`
+
+	// Env defines common env vars. There are four layers for env vars' definitions and
+	// the precedence order is: `original container env vars` > `language specific env vars` > `common env vars` > `instrument spec configs' vars`.
+	// If the former var had been defined, then the other vars would be ignored.
+	// +optional
+	Env []corev1.EnvVar `yaml:"env,omitempty"`
+
+	// Java defines configuration for java auto-instrumentation.
+	// +optional
+	Java Java `yaml:"java,omitempty"`
+
+	// NodeJS defines configuration for nodejs auto-instrumentation.
+	// +optional
+	NodeJS NodeJS `yaml:"nodejs,omitempty"`
+
+	// Python defines configuration for python auto-instrumentation.
+	// +optional
+	Python Python `yaml:"python,omitempty"`
+
+	// DotNet defines configuration for DotNet auto-instrumentation.
+	// +optional
+	DotNet DotNet `yaml:"dotnet,omitempty"`
+
+	// Go defines configuration for Go auto-instrumentation.
+	// When using Go auto-instrumentation you must provide a value for the OTEL_GO_AUTO_TARGET_EXE env var via the
+	// Instrumentation env vars or via the instrumentation.opentelemetry.io/otel-go-auto-target-exe pod annotation.
+	// Failure to set this value causes instrumentation injection to abort, leaving the original pod unchanged.
+	// +optional
+	Go Go `yaml:"go,omitempty"`
+
+	// ApacheHttpd defines configuration for Apache HTTPD auto-instrumentation.
+	// +optional
+	ApacheHttpd ApacheHttpd `yaml:"apacheHttpd,omitempty"`
+
+	// Nginx defines configuration for Nginx auto-instrumentation.
+	// +optional
+	Nginx Nginx `yaml:"nginx,omitempty"`
+
+	// ImagePullPolicy
+	// One of Always, Never, IfNotPresent.
+	// Defaults to Always if :latest tag is specified, or IfNotPresent otherwise.
+	// +optional
+	ImagePullPolicy corev1.PullPolicy `yaml:"imagePullPolicy,omitempty"`
+}
+
+// Resource defines the configuration for the resource attributes, as defined by the OpenTelemetry specification.
+// See also: https://github.com/open-telemetry/opentelemetry-specification/blob/v1.8.0/specification/overview.md#resources
+type Resource struct {
+	// Attributes defines attributes that are added to the resource.
+	// For example environment: dev
+	// +optional
+	Attributes map[string]string `yaml:"resourceAttributes,omitempty"`
+
+	// AddK8sUIDAttributes defines whether K8s UID attributes should be collected (e.g. k8s.deployment.uid).
+	// +optional
+	AddK8sUIDAttributes bool `yaml:"addK8sUIDAttributes,omitempty"`
+}
+
+// Exporter defines OTLP exporter configuration.
+type Exporter struct {
+	// Endpoint is address of the collector with OTLP endpoint.
+	// If the endpoint defines https:// scheme TLS has to be specified.
+	// +optional
+	Endpoint string `yaml:"endpoint,omitempty"`
+
+	// TLS defines certificates for TLS.
+	// TLS needs to be enabled by specifying https:// scheme in the Endpoint.
+	TLS *TLS `yaml:"tls,omitempty"`
+}
+
+type (
+	// SamplerType represents sampler type.
+	SamplerType string
+)
+
+const (
+	// AlwaysOn represents AlwaysOnSampler.
+	AlwaysOn SamplerType = "always_on"
+	// AlwaysOff represents AlwaysOffSampler.
+	AlwaysOff SamplerType = "always_off"
+	// TraceIDRatio represents TraceIdRatioBased.
+	TraceIDRatio SamplerType = "traceidratio"
+	// ParentBasedAlwaysOn represents ParentBased(root=AlwaysOnSampler).
+	ParentBasedAlwaysOn SamplerType = "parentbased_always_on"
+	// ParentBasedAlwaysOff represents ParentBased(root=AlwaysOffSampler).
+	ParentBasedAlwaysOff SamplerType = "parentbased_always_off"
+	// ParentBasedTraceIDRatio represents ParentBased(root=TraceIdRatioBased).
+	ParentBasedTraceIDRatio SamplerType = "parentbased_traceidratio"
+	// JaegerRemote represents JaegerRemoteSampler.
+	JaegerRemote SamplerType = "jaeger_remote"
+	// ParentBasedJaegerRemote represents ParentBased(root=JaegerRemoteSampler).
+	ParentBasedJaegerRemote SamplerType = "parentbased_jaeger_remote"
+	// XRay represents AWS X-Ray Centralized Sampling.
+	XRaySampler SamplerType = "xray"
+)
+
+// TLS defines TLS configuration for exporter.
+type TLS struct {
+	// SecretName defines secret name that will be used to configure TLS on the exporter.
+	// It is user responsibility to create the secret in the namespace of the workload.
+	// The secret must contain client certificate (Cert) and private key (Key).
+	// The CA certificate might be defined in the secret or in the config map.
+	SecretName string `yaml:"secretName,omitempty"`
+
+	// ConfigMapName defines configmap name with CA certificate. If it is not defined CA certificate will be
+	// used from the secret defined in SecretName.
+	ConfigMapName string `yaml:"configMapName,omitempty"`
+
+	// CA defines the key of certificate (e.g. ca.crt) in the configmap map, secret or absolute path to a certificate.
+	// The absolute path can be used when certificate is already present on the workload filesystem e.g.
+	// /var/run/secrets/kubernetes.io/serviceaccount/service-ca.crt
+	CA string `yaml:"ca_file,omitempty"`
+	// Cert defines the key (e.g. tls.crt) of the client certificate in the secret or absolute path to a certificate.
+	// The absolute path can be used when certificate is already present on the workload filesystem.
+	Cert string `yaml:"cert_file,omitempty"`
+	// Key defines a key (e.g. tls.key) of the private key in the secret or absolute path to a certificate.
+	// The absolute path can be used when certificate is already present on the workload filesystem.
+	Key string `yaml:"key_file,omitempty"`
+}
+
+// Sampler defines sampling configuration.
+type Sampler struct {
+	// Type defines sampler type.
+	// The value will be set in the OTEL_TRACES_SAMPLER env var.
+	// The value can be for instance parentbased_always_on, parentbased_always_off, parentbased_traceidratio...
+	// +optional
+	Type SamplerType `yaml:"type,omitempty"`
+
+	// Argument defines sampler argument.
+	// The value depends on the sampler type.
+	// For instance for parentbased_traceidratio sampler type it is a number in range [0..1] e.g. 0.25.
+	// The value will be set in the OTEL_TRACES_SAMPLER_ARG env var.
+	// +optional
+	Argument string `yaml:"argument,omitempty"`
+}
+
+// Defaults defines default values for the instrumentation.
+type Defaults struct {
+	// UseLabelsForResourceAttributes defines whether to use common labels for resource attributes:
+	// Note: first entry wins:
+	//   - `app.kubernetes.io/instance` becomes `service.name`
+	//   - `app.kubernetes.io/name` becomes `service.name`
+	//   - `app.kubernetes.io/version` becomes `service.version`
+	UseLabelsForResourceAttributes bool `yaml:"useLabelsForResourceAttributes,omitempty"`
+}
+
+// Java defines Java SDK and instrumentation configuration.
+type Java struct {
+	// Image is a container image with javaagent auto-instrumentation JAR.
+	// +optional
+	Image string `yaml:"image,omitempty"`
+
+	// VolumeClaimTemplate defines an ephemeral volume used for auto-instrumentation.
+	// If omitted, an emptyDir is used with size limit VolumeSizeLimit
+	VolumeClaimTemplate corev1.PersistentVolumeClaimTemplate `yaml:"volumeClaimTemplate,omitempty"`
+
+	// VolumeSizeLimit defines size limit for volume used for auto-instrumentation.
+	// The default size is 200Mi.
+	VolumeSizeLimit *resource.Quantity `yaml:"volumeLimitSize,omitempty"`
+
+	// Env defines java specific env vars. There are four layers for env vars' definitions and
+	// the precedence order is: `original container env vars` > `language specific env vars` > `common env vars` > `instrument spec configs' vars`.
+	// If the former var had been defined, then the other vars would be ignored.
+	// +optional
+	Env []corev1.EnvVar `yaml:"env,omitempty"`
+
+	// Resources describes the compute resource requirements.
+	// +optional
+	Resources corev1.ResourceRequirements `yaml:"resources,omitempty"`
+
+	// Extensions defines java specific extensions.
+	// All extensions are copied to a single directory; if a JAR with the same name exists, it will be overwritten.
+	// +optional
+	Extensions []Extensions `yaml:"extensions,omitempty"`
+}
+
+type Extensions struct {
+	// Image is a container image with extensions auto-instrumentation JAR.
+	Image string `yaml:"image"`
+
+	// Dir is a directory with extensions auto-instrumentation JAR.
+	Dir string `yaml:"dir"`
+}
+
+// NodeJS defines NodeJS SDK and instrumentation configuration.
+type NodeJS struct {
+	// Image is a container image with NodeJS SDK and auto-instrumentation.
+	// +optional
+	Image string `yaml:"image,omitempty"`
+
+	// VolumeClaimTemplate defines an ephemeral volume used for auto-instrumentation.
+	// If omitted, an emptyDir is used with size limit VolumeSizeLimit
+	VolumeClaimTemplate corev1.PersistentVolumeClaimTemplate `yaml:"volumeClaimTemplate,omitempty"`
+
+	// VolumeSizeLimit defines size limit for volume used for auto-instrumentation.
+	// The default size is 200Mi.
+	VolumeSizeLimit *resource.Quantity `yaml:"volumeLimitSize,omitempty"`
+
+	// Env defines nodejs specific env vars. There are four layers for env vars' definitions and
+	// the precedence order is: `original container env vars` > `language specific env vars` > `common env vars` > `instrument spec configs' vars`.
+	// If the former var had been defined, then the other vars would be ignored.
+	// +optional
+	Env []corev1.EnvVar `yaml:"env,omitempty"`
+
+	// Resources describes the compute resource requirements.
+	// +optional
+	Resources corev1.ResourceRequirements `yaml:"resourceRequirements,omitempty"`
+}
+
+// Python defines Python SDK and instrumentation configuration.
+type Python struct {
+	// Image is a container image with Python SDK and auto-instrumentation.
+	// +optional
+	Image string `yaml:"image,omitempty"`
+
+	// VolumeClaimTemplate defines an ephemeral volume used for auto-instrumentation.
+	// If omitted, an emptyDir is used with size limit VolumeSizeLimit
+	VolumeClaimTemplate corev1.PersistentVolumeClaimTemplate `yaml:"volumeClaimTemplate,omitempty"`
+
+	// VolumeSizeLimit defines size limit for volume used for auto-instrumentation.
+	// The default size is 200Mi.
+	VolumeSizeLimit *resource.Quantity `yaml:"volumeLimitSize,omitempty"`
+
+	// Env defines python specific env vars. There are four layers for env vars' definitions and
+	// the precedence order is: `original container env vars` > `language specific env vars` > `common env vars` > `instrument spec configs' vars`.
+	// If the former var had been defined, then the other vars would be ignored.
+	// +optional
+	Env []corev1.EnvVar `yaml:"env,omitempty"`
+
+	// Resources describes the compute resource requirements.
+	// +optional
+	Resources corev1.ResourceRequirements `yaml:"resourceRequirements,omitempty"`
+}
+
+// DotNet defines DotNet SDK and instrumentation configuration.
+type DotNet struct {
+	// Image is a container image with DotNet SDK and auto-instrumentation.
+	// +optional
+	Image string `yaml:"image,omitempty"`
+
+	// VolumeClaimTemplate defines an ephemeral volume used for auto-instrumentation.
+	// If omitted, an emptyDir is used with size limit VolumeSizeLimit
+	VolumeClaimTemplate corev1.PersistentVolumeClaimTemplate `yaml:"volumeClaimTemplate,omitempty"`
+
+	// VolumeSizeLimit defines size limit for volume used for auto-instrumentation.
+	// The default size is 200Mi.
+	VolumeSizeLimit *resource.Quantity `yaml:"volumeLimitSize,omitempty"`
+
+	// Env defines DotNet specific env vars. There are four layers for env vars' definitions and
+	// the precedence order is: `original container env vars` > `language specific env vars` > `common env vars` > `instrument spec configs' vars`.
+	// If the former var had been defined, then the other vars would be ignored.
+	// +optional
+	Env []corev1.EnvVar `yaml:"env,omitempty"`
+	// Resources describes the compute resource requirements.
+	// +optional
+	Resources corev1.ResourceRequirements `yaml:"resourceRequirements,omitempty"`
+}
+
+type Go struct {
+	// Image is a container image with Go SDK and auto-instrumentation.
+	// +optional
+	Image string `yaml:"image,omitempty"`
+
+	// VolumeClaimTemplate defines an ephemeral volume used for auto-instrumentation.
+	// If omitted, an emptyDir is used with size limit VolumeSizeLimit
+	VolumeClaimTemplate corev1.PersistentVolumeClaimTemplate `yaml:"volumeClaimTemplate,omitempty"`
+
+	// VolumeSizeLimit defines size limit for volume used for auto-instrumentation.
+	// The default size is 200Mi.
+	VolumeSizeLimit *resource.Quantity `yaml:"volumeLimitSize,omitempty"`
+
+	// Env defines Go specific env vars. There are four layers for env vars' definitions and
+	// the precedence order is: `original container env vars` > `language specific env vars` > `common env vars` > `instrument spec configs' vars`.
+	// If the former var had been defined, then the other vars would be ignored.
+	// +optional
+	Env []corev1.EnvVar `yaml:"env,omitempty"`
+
+	// Resources describes the compute resource requirements.
+	// +optional
+	Resources corev1.ResourceRequirements `yaml:"resourceRequirements,omitempty"`
+}
+
+// ApacheHttpd defines Apache SDK and instrumentation configuration.
+type ApacheHttpd struct {
+	// Image is a container image with Apache SDK and auto-instrumentation.
+	// +optional
+	Image string `yaml:"image,omitempty"`
+
+	// VolumeClaimTemplate defines an ephemeral volume used for auto-instrumentation.
+	// If omitted, an emptyDir is used with size limit VolumeSizeLimit
+	VolumeClaimTemplate corev1.PersistentVolumeClaimTemplate `yaml:"volumeClaimTemplate,omitempty"`
+
+	// VolumeSizeLimit defines size limit for volume used for auto-instrumentation.
+	// The default size is 200Mi.
+	VolumeSizeLimit *resource.Quantity `yaml:"volumeLimitSize,omitempty"`
+
+	// Env defines Apache HTTPD specific env vars. There are four layers for env vars' definitions and
+	// the precedence order is: `original container env vars` > `language specific env vars` > `common env vars` > `instrument spec configs' vars`.
+	// If the former var had been defined, then the other vars would be ignored.
+	// +optional
+	Env []corev1.EnvVar `yaml:"env,omitempty"`
+
+	// Attrs defines Apache HTTPD agent specific attributes. The precedence is:
+	// `agent default attributes` > `instrument spec attributes` .
+	// Attributes are documented at https://github.com/open-telemetry/opentelemetry-cpp-contrib/tree/main/instrumentation/otel-webserver-module
+	// +optional
+	Attrs []corev1.EnvVar `yaml:"attrs,omitempty"`
+
+	// Apache HTTPD server version. One of 2.4 or 2.2. Default is 2.4
+	// +optional
+	Version string `yaml:"version,omitempty"`
+
+	// Location of Apache HTTPD server configuration.
+	// Needed only if different from default "/usr/local/apache2/conf"
+	// +optional
+	ConfigPath string `yaml:"configPath,omitempty"`
+
+	// Resources describes the compute resource requirements.
+	// +optional
+	Resources corev1.ResourceRequirements `yaml:"resourceRequirements,omitempty"`
+}
+
+// Nginx defines Nginx SDK and instrumentation configuration.
+type Nginx struct {
+	// Image is a container image with Nginx SDK and auto-instrumentation.
+	// +optional
+	Image string `yaml:"image,omitempty"`
+
+	// VolumeClaimTemplate defines an ephemeral volume used for auto-instrumentation.
+	// If omitted, an emptyDir is used with size limit VolumeSizeLimit
+	VolumeClaimTemplate corev1.PersistentVolumeClaimTemplate `yaml:"volumeClaimTemplate,omitempty"`
+
+	// VolumeSizeLimit defines size limit for volume used for auto-instrumentation.
+	// The default size is 200Mi.
+	VolumeSizeLimit *resource.Quantity `yaml:"volumeLimitSize,omitempty"`
+
+	// Env defines Nginx specific env vars. There are four layers for env vars' definitions and
+	// the precedence order is: `original container env vars` > `language specific env vars` > `common env vars` > `instrument spec configs' vars`.
+	// If the former var had been defined, then the other vars would be ignored.
+	// +optional
+	Env []corev1.EnvVar `yaml:"env,omitempty"`
+
+	// Attrs defines Nginx agent specific attributes. The precedence order is:
+	// `agent default attributes` > `instrument spec attributes` .
+	// Attributes are documented at https://github.com/open-telemetry/opentelemetry-cpp-contrib/tree/main/instrumentation/otel-webserver-module
+	// +optional
+	Attrs []corev1.EnvVar `yaml:"attrs,omitempty"`
+
+	// Location of Nginx configuration file.
+	// Needed only if different from default "/etx/nginx/nginx.conf"
+	// +optional
+	ConfigFile string `yaml:"configFile,omitempty"`
+
+	// Resources describes the compute resource requirements.
+	// +optional
+	Resources corev1.ResourceRequirements `yaml:"resourceRequirements,omitempty"`
+}
diff --git a/internal/config/testdata/config.yaml b/internal/config/testdata/config.yaml
index 05699f2998..7f9eeed173 100644
--- a/internal/config/testdata/config.yaml
+++ b/internal/config/testdata/config.yaml
@@ -47,3 +47,4 @@ zap:
   level-key: level
   level-format: uppercase
 enable-webhooks: true
+enable-instrumentation-crds: true
diff --git a/internal/controllers/reconcile_test.go b/internal/controllers/reconcile_test.go
index 3c825b46b5..1646cb8410 100644
--- a/internal/controllers/reconcile_test.go
+++ b/internal/controllers/reconcile_test.go
@@ -620,6 +620,7 @@ func TestOpenTelemetryCollectorReconciler_Reconcile(t *testing.T) {
 				PrometheusCRAvailability:      prometheus.Available,
 				TargetAllocatorConfigMapEntry: "remoteconfiguration.yaml",
 				CollectorConfigMapEntry:       "collector.yaml",
+				EnableInstrumentationCRDs:     true,
 			}
 			reconciler := createTestReconciler(t, testCtx, cfg)
 
@@ -789,6 +790,7 @@ func TestOpenTelemetryCollectorReconciler_RemoveDisabled(t *testing.T) {
 		TargetAllocatorImage:        "default-ta-allocator",
 		OpenShiftRoutesAvailability: openshift.RoutesAvailable,
 		PrometheusCRAvailability:    prometheus.Available,
+		EnableInstrumentationCRDs:   true,
 	}
 	reconciler := createTestReconciler(t, testCtx, cfg)
 
@@ -904,6 +906,7 @@ func TestOpenTelemetryCollectorReconciler_VersionedConfigMaps(t *testing.T) {
 		CollectorImage:              "default-collector",
 		TargetAllocatorImage:        "default-ta-allocator",
 		OpenShiftRoutesAvailability: openshift.RoutesAvailable,
+		EnableInstrumentationCRDs:   true,
 	}
 	reconciler := createTestReconciler(t, testCtx, cfg)
 
@@ -1100,6 +1103,7 @@ func TestOpAMPBridgeReconciler_Reconcile(t *testing.T) {
 				OperatorOpAMPBridgeConfigMapEntry: "remoteconfiguration.yaml",
 				CollectorConfigMapEntry:           "collector.yaml",
 				TargetAllocatorConfigMapEntry:     "targetallocator.yaml",
+				EnableInstrumentationCRDs:         true,
 			}
 			reconciler := controllers.NewOpAMPBridgeReconciler(controllers.OpAMPBridgeReconcilerParams{
 				Client:   k8sClient,
@@ -1248,6 +1252,7 @@ service:
 		CreateRBACPermissions:             autoRBAC.Available,
 		CollectorConfigMapEntry:           "collector.yaml",
 		OperatorOpAMPBridgeConfigMapEntry: "remoteconfiguration.yaml",
+		EnableInstrumentationCRDs:         true,
 	}
 	reconciler := createTestReconciler(t, testCtx, cfg)
 
@@ -1304,6 +1309,7 @@ func TestUpgrade(t *testing.T) {
 		TargetAllocatorImage:          "default-ta-allocator",
 		CollectorConfigMapEntry:       "collector.yaml",
 		TargetAllocatorConfigMapEntry: "remoteconfiguration.yaml",
+		EnableInstrumentationCRDs:     true,
 	}
 	reconciler := createTestReconcilerWithVersion(
 		t, testCtx,
diff --git a/internal/instrumentation/podmutator.go b/internal/instrumentation/podmutator.go
index 478b7face6..314564d3c7 100644
--- a/internal/instrumentation/podmutator.go
+++ b/internal/instrumentation/podmutator.go
@@ -414,7 +414,143 @@ func (pm *instPodMutator) Mutate(ctx context.Context, ns corev1.Namespace, pod c
 	return modifiedPod, nil
 }
 
+func ConvertConfig(cfg *config.InstrumentationSpec) *v1alpha1.InstrumentationSpec {
+	if cfg == nil {
+		return nil
+	}
+	var tls *v1alpha1.TLS
+	if cfg.TLS != nil {
+		tls = &v1alpha1.TLS{
+			SecretName:    cfg.TLS.SecretName,
+			ConfigMapName: cfg.TLS.ConfigMapName,
+			CA:            cfg.TLS.CA,
+			Cert:          cfg.TLS.Cert,
+			Key:           cfg.TLS.Key,
+		}
+	}
+	return &v1alpha1.InstrumentationSpec{
+		Exporter: v1alpha1.Exporter{
+			Endpoint: cfg.Exporter.Endpoint,
+			TLS:      tls,
+		},
+		Resource: v1alpha1.Resource{
+			Attributes:          cfg.Resource.Attributes,
+			AddK8sUIDAttributes: cfg.Resource.AddK8sUIDAttributes,
+		},
+		Propagators: func() []v1alpha1.Propagator {
+			result := make([]v1alpha1.Propagator, len(cfg.Propagators))
+			for i, p := range cfg.Propagators {
+				result[i] = v1alpha1.Propagator(p)
+			}
+			return result
+		}(),
+		Sampler: v1alpha1.Sampler{
+			Type:     v1alpha1.SamplerType(cfg.Sampler.Type),
+			Argument: cfg.Sampler.Argument,
+		},
+		Defaults: v1alpha1.Defaults{
+			UseLabelsForResourceAttributes: cfg.Defaults.UseLabelsForResourceAttributes,
+		},
+		Env: cfg.Env,
+		Java: v1alpha1.Java{
+			Image:               cfg.Java.Image,
+			VolumeClaimTemplate: cfg.Java.VolumeClaimTemplate,
+			VolumeSizeLimit:     cfg.Java.VolumeSizeLimit,
+			Env:                 cfg.Java.Env,
+			Resources:           cfg.Java.Resources,
+			Extensions: func() []v1alpha1.Extensions {
+				result := make([]v1alpha1.Extensions, len(cfg.Java.Extensions))
+				for _, ext := range cfg.Java.Extensions {
+					result = append(result, v1alpha1.Extensions{
+						Image: ext.Image,
+						Dir:   ext.Dir,
+					})
+				}
+				return result
+			}(),
+		},
+		NodeJS: v1alpha1.NodeJS{
+			Image:               cfg.NodeJS.Image,
+			VolumeClaimTemplate: cfg.NodeJS.VolumeClaimTemplate,
+			VolumeSizeLimit:     cfg.NodeJS.VolumeSizeLimit,
+			Env:                 cfg.NodeJS.Env,
+			Resources:           cfg.NodeJS.Resources,
+		},
+		Python: v1alpha1.Python{
+			Image:               cfg.Python.Image,
+			VolumeClaimTemplate: cfg.Python.VolumeClaimTemplate,
+			VolumeSizeLimit:     cfg.Python.VolumeSizeLimit,
+			Env:                 cfg.Python.Env,
+			Resources:           cfg.Python.Resources,
+		},
+		DotNet: v1alpha1.DotNet{
+			Image:               cfg.DotNet.Image,
+			VolumeClaimTemplate: cfg.DotNet.VolumeClaimTemplate,
+			VolumeSizeLimit:     cfg.DotNet.VolumeSizeLimit,
+			Env:                 cfg.DotNet.Env,
+			Resources:           cfg.DotNet.Resources,
+		},
+		Go: v1alpha1.Go{
+			Image:               cfg.Go.Image,
+			VolumeClaimTemplate: cfg.Go.VolumeClaimTemplate,
+			VolumeSizeLimit:     cfg.Go.VolumeSizeLimit,
+			Env:                 cfg.Go.Env,
+			Resources:           cfg.Go.Resources,
+		},
+		ApacheHttpd: v1alpha1.ApacheHttpd{
+			Image:               cfg.ApacheHttpd.Image,
+			VolumeClaimTemplate: cfg.ApacheHttpd.VolumeClaimTemplate,
+			VolumeSizeLimit:     cfg.ApacheHttpd.VolumeSizeLimit,
+			Env:                 cfg.ApacheHttpd.Env,
+			Attrs:               cfg.ApacheHttpd.Attrs,
+			Version:             cfg.ApacheHttpd.Version,
+			ConfigPath:          cfg.ApacheHttpd.ConfigPath,
+			Resources:           cfg.ApacheHttpd.Resources,
+		},
+		Nginx: v1alpha1.Nginx{
+			Image:               cfg.Nginx.Image,
+			VolumeClaimTemplate: cfg.Nginx.VolumeClaimTemplate,
+			VolumeSizeLimit:     cfg.Nginx.VolumeSizeLimit,
+			Env:                 cfg.Nginx.Env,
+			Attrs:               cfg.Nginx.Attrs,
+			ConfigFile:          cfg.Nginx.ConfigFile,
+			Resources:           cfg.Nginx.Resources,
+		},
+		ImagePullPolicy: cfg.ImagePullPolicy,
+	}
+}
+
 func (pm *instPodMutator) getInstrumentationInstance(ctx context.Context, ns corev1.Namespace, pod corev1.Pod, instAnnotation string) (*v1alpha1.Instrumentation, error) {
+	if !pm.config.EnableInstrumentationCRDs {
+		var instr *v1alpha1.InstrumentationSpec
+		switch instAnnotation {
+		case annotationInjectDotNet:
+			instr = ConvertConfig(pm.config.Instrumentation.DotNet)
+
+		case annotationInjectJava:
+			instr = ConvertConfig(pm.config.Instrumentation.Java)
+		case annotationInjectNodeJS:
+			instr = ConvertConfig(pm.config.Instrumentation.NodeJS)
+		case annotationInjectGo:
+			instr = ConvertConfig(pm.config.Instrumentation.Go)
+		case annotationInjectApacheHttpd:
+			instr = ConvertConfig(pm.config.Instrumentation.ApacheHttpd)
+		case annotationInjectNginx:
+			instr = ConvertConfig(pm.config.Instrumentation.Nginx)
+		case annotationInjectPython:
+			instr = ConvertConfig(pm.config.Instrumentation.Python)
+		case annotationInjectSdk:
+			instr = ConvertConfig(pm.config.Instrumentation.Sdk)
+		default:
+			panic("Unknown instrumentation annotation: " + instAnnotation)
+		}
+		if instr == nil {
+			return nil, nil
+		}
+		return &v1alpha1.Instrumentation{
+			Spec: *instr,
+		}, nil
+	}
 	instValue := annotationValue(ns.ObjectMeta, pod.ObjectMeta, instAnnotation)
 
 	if len(instValue) == 0 || strings.EqualFold(instValue, "false") {
diff --git a/internal/instrumentation/podmutator_test.go b/internal/instrumentation/podmutator_test.go
index e674608a2d..35ac7f340d 100644
--- a/internal/instrumentation/podmutator_test.go
+++ b/internal/instrumentation/podmutator_test.go
@@ -680,6 +680,7 @@ func TestMutatePod(t *testing.T) {
 				},
 			},
 			config: config.Config{
+				EnableInstrumentationCRDs:     true,
 				EnableJavaAutoInstrumentation: false,
 			},
 		},
@@ -866,6 +867,7 @@ func TestMutatePod(t *testing.T) {
 				},
 			},
 			config: config.Config{
+				EnableInstrumentationCRDs:       true,
 				EnableNodeJSAutoInstrumentation: true,
 			},
 		},
@@ -1140,6 +1142,7 @@ func TestMutatePod(t *testing.T) {
 				},
 			},
 			config: config.Config{
+				EnableInstrumentationCRDs:       true,
 				EnableNodeJSAutoInstrumentation: true,
 			},
 		},
@@ -1428,6 +1431,7 @@ func TestMutatePod(t *testing.T) {
 				},
 			},
 			config: config.Config{
+				EnableInstrumentationCRDs:       true,
 				EnablePythonAutoInstrumentation: true,
 			},
 		},
@@ -1734,6 +1738,7 @@ func TestMutatePod(t *testing.T) {
 				},
 			},
 			config: config.Config{
+				EnableInstrumentationCRDs:       true,
 				EnablePythonAutoInstrumentation: true,
 			},
 		},
@@ -2028,6 +2033,7 @@ func TestMutatePod(t *testing.T) {
 				},
 			},
 			config: config.Config{
+				EnableInstrumentationCRDs:       true,
 				EnableDotNetAutoInstrumentation: true,
 			},
 		},
@@ -2226,6 +2232,7 @@ func TestMutatePod(t *testing.T) {
 				},
 			},
 			config: config.Config{
+				EnableInstrumentationCRDs:       true,
 				EnableDotNetAutoInstrumentation: true,
 			},
 		},
@@ -2536,6 +2543,7 @@ func TestMutatePod(t *testing.T) {
 				},
 			},
 			config: config.Config{
+				EnableInstrumentationCRDs:       true,
 				EnableDotNetAutoInstrumentation: true,
 			},
 		},
@@ -2617,6 +2625,7 @@ func TestMutatePod(t *testing.T) {
 				},
 			},
 			config: config.Config{
+				EnableInstrumentationCRDs:       true,
 				EnableDotNetAutoInstrumentation: false,
 			},
 		},
@@ -2795,6 +2804,7 @@ func TestMutatePod(t *testing.T) {
 				},
 			},
 			config: config.Config{
+				EnableInstrumentationCRDs:   true,
 				EnableGoAutoInstrumentation: true,
 			},
 		},
@@ -2878,6 +2888,7 @@ func TestMutatePod(t *testing.T) {
 				},
 			},
 			config: config.Config{
+				EnableInstrumentationCRDs:   true,
 				EnableGoAutoInstrumentation: false,
 			},
 		},
@@ -3049,6 +3060,7 @@ func TestMutatePod(t *testing.T) {
 				},
 			},
 			config: config.Config{
+				EnableInstrumentationCRDs:        true,
 				EnableApacheHttpdInstrumentation: true,
 			},
 		},
@@ -3126,6 +3138,7 @@ func TestMutatePod(t *testing.T) {
 				},
 			},
 			config: config.Config{
+				EnableInstrumentationCRDs:        true,
 				EnableApacheHttpdInstrumentation: false,
 			},
 		},
@@ -3306,6 +3319,7 @@ func TestMutatePod(t *testing.T) {
 				},
 			},
 			config: config.Config{
+				EnableInstrumentationCRDs:      true,
 				EnableNginxAutoInstrumentation: true,
 			},
 		},
@@ -3389,6 +3403,7 @@ func TestMutatePod(t *testing.T) {
 				},
 			},
 			config: config.Config{
+				EnableInstrumentationCRDs:       true,
 				EnableMultiInstrumentation:      true,
 				EnableNodeJSAutoInstrumentation: true,
 				EnablePythonAutoInstrumentation: true,
@@ -3522,6 +3537,9 @@ func TestMutatePod(t *testing.T) {
 				},
 			},
 			err: `instrumentations.opentelemetry.io "doesnotexists" not found`,
+			config: config.Config{
+				EnableInstrumentationCRDs: true,
+			},
 		},
 		{
 			name: "multi instrumentation for multiple containers feature gate enabled",
@@ -4294,6 +4312,7 @@ func TestMutatePod(t *testing.T) {
 				},
 			},
 			config: config.Config{
+				EnableInstrumentationCRDs:       true,
 				EnableMultiInstrumentation:      true,
 				EnableJavaAutoInstrumentation:   true,
 				EnableNodeJSAutoInstrumentation: true,
@@ -4454,6 +4473,7 @@ func TestMutatePod(t *testing.T) {
 				},
 			},
 			config: config.Config{
+				EnableInstrumentationCRDs:       true,
 				EnableMultiInstrumentation:      false,
 				EnableJavaAutoInstrumentation:   false,
 				EnableNodeJSAutoInstrumentation: false,
@@ -4604,6 +4624,7 @@ func TestMutatePod(t *testing.T) {
 				},
 			},
 			config: config.Config{
+				EnableInstrumentationCRDs:     true,
 				EnableMultiInstrumentation:    true,
 				EnableJavaAutoInstrumentation: false,
 			},
@@ -4802,6 +4823,7 @@ func TestMutatePod(t *testing.T) {
 				},
 			},
 			config: config.Config{
+				EnableInstrumentationCRDs:       true,
 				EnableMultiInstrumentation:      true,
 				EnableDotNetAutoInstrumentation: true,
 			},
@@ -4905,6 +4927,7 @@ func TestMutatePod(t *testing.T) {
 				},
 			},
 			config: config.Config{
+				EnableInstrumentationCRDs:       true,
 				EnableMultiInstrumentation:      true,
 				EnableDotNetAutoInstrumentation: false,
 				EnableNodeJSAutoInstrumentation: false,
@@ -4992,6 +5015,7 @@ func TestMutatePod(t *testing.T) {
 				require.NoError(t, err)
 				assert.Equal(t, test.expected, pod)
 			} else {
+				require.Error(t, err)
 				assert.Contains(t, err.Error(), test.err)
 			}
 		})
diff --git a/internal/instrumentation/upgrade/upgrade.go b/internal/instrumentation/upgrade/upgrade.go
index ce60b525ea..55aec6634c 100644
--- a/internal/instrumentation/upgrade/upgrade.go
+++ b/internal/instrumentation/upgrade/upgrade.go
@@ -7,13 +7,16 @@ import (
 	"context"
 	"fmt"
 	"reflect"
+	"strconv"
 
 	"github.com/go-logr/logr"
+	metav1 "k8s.io/apimachinery/pkg/apis/meta/v1"
 	"k8s.io/client-go/tools/record"
 	"sigs.k8s.io/controller-runtime/pkg/client"
 
 	"github.com/open-telemetry/opentelemetry-operator/apis/v1alpha1"
 	"github.com/open-telemetry/opentelemetry-operator/internal/config"
+	"github.com/open-telemetry/opentelemetry-operator/internal/instrumentation"
 	"github.com/open-telemetry/opentelemetry-operator/pkg/constants"
 )
 
@@ -66,13 +69,100 @@ func NewInstrumentationUpgrade(client client.Client, logger logr.Logger, recorde
 // +kubebuilder:rbac:groups=opentelemetry.io,resources=instrumentations,verbs=get;list;watch;update;patch
 
 // ManagedInstances upgrades managed instances by the opentelemetry-operator.
-func (u *InstrumentationUpgrade) ManagedInstances(ctx context.Context) error {
-	u.Logger.Info("looking for managed Instrumentation instances to upgrade")
+func (u *InstrumentationUpgrade) ManagedInstances(ctx context.Context, cfg config.Config) error {
 	list := &v1alpha1.InstrumentationList{}
-	if err := u.Client.List(ctx, list); err != nil {
-		return fmt.Errorf("failed to list: %w", err)
+	if cfg.EnableInstrumentationCRDs {
+		u.Logger.Info("looking for managed Instrumentation instances to upgrade")
+		if err := u.Client.List(ctx, list); err != nil {
+			return fmt.Errorf("failed to list: %w", err)
+		}
+	} else {
+		list.Items = []v1alpha1.Instrumentation{}
+		if instr := instrumentation.ConvertConfig(cfg.Instrumentation.Java); instr != nil {
+			list.Items = append(list.Items, v1alpha1.Instrumentation{
+				Status:   v1alpha1.InstrumentationStatus{},
+				TypeMeta: metav1.TypeMeta{},
+				Spec:     *instr,
+				ObjectMeta: metav1.ObjectMeta{
+					Annotations: map[string]string{
+						"enable-java-instrumentation": strconv.FormatBool(cfg.EnableJavaAutoInstrumentation),
+					},
+				},
+			})
+		}
+		if instr := instrumentation.ConvertConfig(cfg.Instrumentation.NodeJS); instr != nil {
+			list.Items = append(list.Items, v1alpha1.Instrumentation{
+				Status:   v1alpha1.InstrumentationStatus{},
+				TypeMeta: metav1.TypeMeta{},
+				Spec:     *instr,
+				ObjectMeta: metav1.ObjectMeta{
+					Annotations: map[string]string{
+						"enable-nodejs-instrumentation": strconv.FormatBool(cfg.EnableNodeJSAutoInstrumentation),
+					},
+				},
+			})
+		}
+		if instr := instrumentation.ConvertConfig(cfg.Instrumentation.DotNet); instr != nil {
+			list.Items = append(list.Items, v1alpha1.Instrumentation{
+				Status:   v1alpha1.InstrumentationStatus{},
+				TypeMeta: metav1.TypeMeta{},
+				Spec:     *instr,
+				ObjectMeta: metav1.ObjectMeta{
+					Annotations: map[string]string{
+						"enable-dotnet-instrumentation": strconv.FormatBool(cfg.EnableDotNetAutoInstrumentation),
+					},
+				},
+			})
+		}
+		if instr := instrumentation.ConvertConfig(cfg.Instrumentation.Go); instr != nil {
+			list.Items = append(list.Items, v1alpha1.Instrumentation{
+				Status:   v1alpha1.InstrumentationStatus{},
+				TypeMeta: metav1.TypeMeta{},
+				Spec:     *instr,
+				ObjectMeta: metav1.ObjectMeta{
+					Annotations: map[string]string{
+						"enable-go-instrumentation": strconv.FormatBool(cfg.EnableGoAutoInstrumentation),
+					},
+				},
+			})
+		}
+		if instr := instrumentation.ConvertConfig(cfg.Instrumentation.Python); instr != nil {
+			list.Items = append(list.Items, v1alpha1.Instrumentation{
+				Status:   v1alpha1.InstrumentationStatus{},
+				TypeMeta: metav1.TypeMeta{},
+				Spec:     *instr,
+				ObjectMeta: metav1.ObjectMeta{
+					Annotations: map[string]string{
+						"enable-python-instrumentation": strconv.FormatBool(cfg.EnablePythonAutoInstrumentation),
+					},
+				},
+			})
+		}
+		if instr := instrumentation.ConvertConfig(cfg.Instrumentation.ApacheHttpd); instr != nil {
+			list.Items = append(list.Items, v1alpha1.Instrumentation{
+				Status:   v1alpha1.InstrumentationStatus{},
+				TypeMeta: metav1.TypeMeta{},
+				Spec:     *instr,
+				ObjectMeta: metav1.ObjectMeta{
+					Annotations: map[string]string{
+						"enable-apache-httpd-instrumentation": strconv.FormatBool(cfg.EnableApacheHttpdInstrumentation),
+					},
+				},
+			})
+		}
+		if instr := instrumentation.ConvertConfig(cfg.Instrumentation.Nginx); instr != nil {
+			list.Items = append(list.Items, v1alpha1.Instrumentation{
+				Status:   v1alpha1.InstrumentationStatus{},
+				TypeMeta: metav1.TypeMeta{},
+				Spec:     *instr,
+				ObjectMeta: metav1.ObjectMeta{
+					Annotations: map[string]string{
+						"enable-nginx-instrumentation": strconv.FormatBool(cfg.EnableNginxAutoInstrumentation),
+					},
+				},
+			})
+		}
 	}
-
 	for i := range list.Items {
 		toUpgrade := list.Items[i]
 		upgraded := u.upgrade(ctx, toUpgrade)
diff --git a/internal/instrumentation/upgrade/upgrade_test.go b/internal/instrumentation/upgrade/upgrade_test.go
index 172b535f39..197ae1c7d1 100644
--- a/internal/instrumentation/upgrade/upgrade_test.go
+++ b/internal/instrumentation/upgrade/upgrade_test.go
@@ -44,6 +44,7 @@ func TestUpgrade(t *testing.T) {
 	}
 
 	cfg := config.Config{
+		EnableInstrumentationCRDs:           true,
 		AutoInstrumentationJavaImage:        "java:1",
 		AutoInstrumentationNodeJSImage:      "nodejs:1",
 		AutoInstrumentationPythonImage:      "python:1",
@@ -76,6 +77,7 @@ func TestUpgrade(t *testing.T) {
 	require.NoError(t, err)
 
 	cfg = config.Config{
+		EnableInstrumentationCRDs:           true,
 		AutoInstrumentationJavaImage:        "java:2",
 		AutoInstrumentationNodeJSImage:      "nodejs:2",
 		AutoInstrumentationPythonImage:      "python:2",
@@ -93,7 +95,7 @@ func TestUpgrade(t *testing.T) {
 	}
 	up := NewInstrumentationUpgrade(k8sClient, ctrl.Log.WithName("instrumentation-upgrade"), &record.FakeRecorder{}, cfg)
 
-	err = up.ManagedInstances(context.Background())
+	err = up.ManagedInstances(context.Background(), cfg)
 	require.NoError(t, err)
 
 	updated := v1alpha1.Instrumentation{}
diff --git a/main.go b/main.go
index b00c81e7a1..5b1443e3f2 100644
--- a/main.go
+++ b/main.go
@@ -418,7 +418,7 @@ func addDependencies(_ context.Context, mgr ctrl.Manager, cfg config.Config) err
 			mgr.GetEventRecorderFor("opentelemetry-operator"),
 			cfg,
 		)
-		return u.ManagedInstances(c)
+		return u.ManagedInstances(c, cfg)
 	}))
 	if err != nil {
 		return fmt.Errorf("failed to upgrade Instrumentation instances: %w", err)
diff --git a/tests/e2e-targetallocator/targetallocator-metrics/chainsaw-test.yaml b/tests/e2e-targetallocator/targetallocator-metrics/chainsaw-test.yaml
index 9263263154..18c9c7ad04 100644
--- a/tests/e2e-targetallocator/targetallocator-metrics/chainsaw-test.yaml
+++ b/tests/e2e-targetallocator/targetallocator-metrics/chainsaw-test.yaml
@@ -52,7 +52,7 @@ spec:
         - assert:
             resource:
               (length($metrics[?as_string(metric."__name__") == 'otel_scope_info']) >= `0`): true
-              (length($metrics[?as_string(metric."__name__") == 'otelcol_exporter_sent_metric_points_total']) >= `0`): true
+              (length($metrics[?as_string(metric."__name__") == 'otelcol_process_cpu_seconds_total']) >= `0`): true
     - name: Assert Target Allocator metrics
       try:
         - command:
diff --git a/tests/integration/certs.yaml b/tests/integration/certs.yaml
new file mode 100644
index 0000000000..359ae5dbc0
--- /dev/null
+++ b/tests/integration/certs.yaml
@@ -0,0 +1,69 @@
+---
+apiVersion: certificates.k8s.io/v1
+kind: CertificateSigningRequest
+metadata:
+  name: operator
+spec:
+  request: "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"
+  signerName: example.com/serving
+  usages:
+    - digital signature
+    - key encipherment
+    - server auth
+---
+apiVersion: v1
+kind: ConfigMap
+metadata:
+  name: certs
+data:
+  tls.key: |
+    -----BEGIN PRIVATE KEY-----
+    MIIEvgIBADANBgkqhkiG9w0BAQEFAASCBKgwggSkAgEAAoIBAQDMNnY9jT6zEK2O
+    EgLjwNPyJfjwFrMsXbYOoSs5L6OVOVDY8uHV5Xp/IFC3xIRKSr7cAaP+PyOvCH4m
+    iNt3B/rWA12hQ3PpvT7psDuWo51lSms7SrQ3tYLSPxvOfdySe9KTOKn9kkrrz2Yn
+    XJLdB3OqW23PXX2z1ulapDO0uNNy+3D9b0YK2qkzjz2jbgotahVZuJYLkN9PdOlb
+    ksgvLAH0wwkHYMygSWzjfNCpXwgGwbHxPfAJYUDeMXXSp2HYme74H0D3b63X+YzL
+    VxS7Q922BfS2GPo5NLPbYYix3FodEeZzjIDcIjAzzJ8JCOqtB9cRn9TKveGC7XLW
+    nP98jHODAgMBAAECggEAM0IQV87WSBgNmDWJKCXEjWlenNT10FMNWYq20LnWc6RZ
+    WLtOWGQrZTF1UUswcX1lfs+inDS4/jxBfeaoP65vFbzuiYXm2Gq6Geo0atFStpQB
+    anaL2dfjqGZS0nfhH5uY9X8pnA5WY+5BE+w2qOgv7jjYzU4IOVXeaPQCToB+AsQL
+    XSBw+bZTyOhBrNy8gtM1wxNeKyVTbke2rI4OZybnRiRW5+1QthpdY9LtKYQPIH94
+    B4tllHK7dfo5Mn47s0Mqlu+trxksbMU4ALnaSwafUQtY2JRkYRugUIKmngb4kx1w
+    fgOzh1nSHzpFPq5+rFT+tOj9wRvFP+mRykTkRoBJIQKBgQDxB0TZvoP6cSnOuUDR
+    +SFp0bBW//4gbNDzvM+a9FQfRz8bagQgjI5nlWN96jNJbTyVmXfIVbAlr3T8JVIX
+    MwBKkDkvbAhocek54LUXLa08gQgwz3XJX4WxX5lrGc1YhQcnOFmPGUBP1tLwEAx2
+    KQgjnPDyUe7aMsNkIYgIwAxBqQKBgQDY5cQdZRfxeKlOlwlPvcQB/bpaZVA5LhmQ
+    hfHZRJiaPAp+prohJVSQ/UtjLHYnS1NdiH41Zi/I6L3rfRlPumC/q19p7ScJjAKd
+    9XdlZvrIjb+Ud9h+DBMFp/axDUfEpou7yPAAn1kff6xU2h1VMP6gaLRyFFCQTCrn
+    BqYe3YvfSwKBgQCNXm0Upbi1IMCbvm51eYEOlu2t6ZH9JLXd7+V4hkv82IX8J09q
+    Y+Z2fNmRFdek/owlVpE6EIAzaljcN2uRrdlC4pqX5O59jCp2RwUQJjtQnIHYVyZH
+    yV4Z7e+HMOgPPl82ssdctjvRWDf6k/8rIt/iO3/bMRE+K74Msdoe/71wmQKBgGdN
+    2ABgG+1ImOrziN3P9kE0hcN0KadyS37ILQ5cW4pqOl1kL5aF3ydHXNaZYJUKjWQp
+    FGN+jhfUslAsvxd4H4hqqQEckNE9PCnbtcg4Kg3HZY3jHtu6CH1TKG3fc2U4JamE
+    5LqHKr2T45JuaDYhJcVk2TzUbCKuBGkQg6KDxpDNAoGBAIjjqCojvwrJCS+LywEv
+    F3bqXzIvXeDjbwDOe/mQhwBLzvpsHqTkZZWuy7eOuQsOFgJLz0Az0LNRUN4RV6N7
+    2TpKG+XuegomTsDjDkunKzewSaKmWHYOxo5jy52STmtv72jW4YhjRLYZ3MMedMpB
+    jWuuCAvDcrNaABMyOGHzZraD
+    -----END PRIVATE KEY-----
+  tls.crt: |
+    -----BEGIN CERTIFICATE-----
+    MIIDWjCCAkKgAwIBAgIUdU5Qo8rswpglH+/B7g4/7kQRLAkwDQYJKoZIhvcNAQEL
+    BQAwJzElMCMGA1UEAwwcb3BlcmF0b3Itd2ViaG9vay5kZWZhdWx0LnN2YzAgFw0y
+    NDEyMjcyMDE3MDFaGA8yMDUyMDUxNDIwMTcwMVowJzElMCMGA1UEAwwcb3BlcmF0
+    b3Itd2ViaG9vay5kZWZhdWx0LnN2YzCCASIwDQYJKoZIhvcNAQEBBQADggEPADCC
+    AQoCggEBAMw2dj2NPrMQrY4SAuPA0/Il+PAWsyxdtg6hKzkvo5U5UNjy4dXlen8g
+    ULfEhEpKvtwBo/4/I68IfiaI23cH+tYDXaFDc+m9PumwO5ajnWVKaztKtDe1gtI/
+    G8593JJ70pM4qf2SSuvPZidckt0Hc6pbbc9dfbPW6VqkM7S403L7cP1vRgraqTOP
+    PaNuCi1qFVm4lguQ30906VuSyC8sAfTDCQdgzKBJbON80KlfCAbBsfE98AlhQN4x
+    ddKnYdiZ7vgfQPdvrdf5jMtXFLtD3bYF9LYY+jk0s9thiLHcWh0R5nOMgNwiMDPM
+    nwkI6q0H1xGf1Mq94YLtctac/3yMc4MCAwEAAaN8MHowDgYDVR0PAQH/BAQDAgWg
+    MCAGA1UdJQEB/wQWMBQGCCsGAQUFBwMBBggrBgEFBQcDAjAnBgNVHREEIDAeghxv
+    cGVyYXRvci13ZWJob29rLmRlZmF1bHQuc3ZjMB0GA1UdDgQWBBTeVi00CIUEE+Bk
+    kEiDl25qjVcfGTANBgkqhkiG9w0BAQsFAAOCAQEAWYfXUwV9wgJhfPIZuI9puX59
+    fXlzksS/X2EE9C9gDg5zuPLZ8MmfBglFR+xBO3PXLBKxCU0U2nwZwuKT1qbTXcHf
+    kPywNOnMDAvbfO3I8zg+4eNeMM5WWrrL7JA6L6kSMY3wk1VPriRTajrmJP53T9rI
+    1XZLRM6C0xl34gniOqRK+CnmpYUw0yQUi0neeMgQFmhzClaafdNWd6aerBQik1jg
+    kn4iNr5FKfmDHNr/WrmcDJ8GTCgKU4R+f4zFFhgO7dHpUs5zD4szirq6n2ayEd8b
+    aSU0+wL2C4Kd72AYDHrkaG2Qi19xCZJDIFqT14m5Rexpbx4i+9E6LgonqX0g4w==
+    -----END CERTIFICATE-----
+
diff --git a/tests/integration/collector.yaml b/tests/integration/collector.yaml
new file mode 100644
index 0000000000..38557086a1
--- /dev/null
+++ b/tests/integration/collector.yaml
@@ -0,0 +1,80 @@
+apiVersion: apps/v1
+kind: Deployment
+metadata:
+  name: collector
+spec:
+  replicas: 1
+  selector:
+    matchLabels:
+      app: collector
+  template:
+    metadata:
+      name: collector
+      labels:
+        app: collector
+    spec:
+      automountServiceAccountToken: false
+      containers:
+        - image: otel/opentelemetry-collector-contrib:latest
+          name: collector
+          imagePullPolicy: IfNotPresent
+          volumeMounts:
+            - name: config-volume
+              mountPath: /etc/otelcol-contrib/config.yaml
+              subPath: config.yaml
+          ports:
+            - containerPort: 4317
+              name: otlp
+            - containerPort: 4318
+              name: otlphttp
+      volumes:
+        - name: config-volume
+          configMap:
+            name: collector-config
+---
+apiVersion: v1
+kind: Service
+metadata:
+  name: collector
+  namespace: default
+spec:
+  ports:
+    - port: 4317
+      protocol: TCP
+      targetPort: otlp
+      name: otlp
+    - port: 4318
+      protocol: TCP
+      targetPort: otlphttp
+      name: otlphttp
+  selector:
+    app: collector
+---
+apiVersion: v1
+kind: ConfigMap
+metadata:
+  name: collector-config
+  namespace: default
+data:
+  config.yaml: |
+    receivers:
+      otlp:
+        protocols:
+          grpc:
+            endpoint: "0.0.0.0:4317"
+          http:
+            endpoint: "0.0.0.0:4318"
+    exporters:
+      debug:
+        verbosity: detailed
+    service:
+      pipelines:
+       metrics:
+         receivers: [otlp]
+         exporters: [debug]
+       traces:
+         receivers: [otlp]
+         exporters: [debug]
+       logs:
+         receivers: [otlp]
+         exporters: [debug]
\ No newline at end of file
diff --git a/tests/integration/java.yaml b/tests/integration/java.yaml
new file mode 100644
index 0000000000..a39e03dd81
--- /dev/null
+++ b/tests/integration/java.yaml
@@ -0,0 +1,22 @@
+apiVersion: apps/v1
+kind: Deployment
+metadata:
+  name: java-app
+spec:
+  replicas: 1
+  selector:
+    matchLabels:
+      app: java-app
+  template:
+    metadata:
+      name: java-app
+      labels:
+        app: java-app
+      annotations:
+        instrumentation.opentelemetry.io/inject-java: "true"
+    spec:
+      automountServiceAccountToken: false
+      containers:
+        - image: tomcat:latest
+          name: java-app
+          imagePullPolicy: IfNotPresent
diff --git a/tests/integration/operator.yaml b/tests/integration/operator.yaml
new file mode 100644
index 0000000000..a68390c643
--- /dev/null
+++ b/tests/integration/operator.yaml
@@ -0,0 +1,166 @@
+---
+apiVersion: v1
+kind: ConfigMap
+metadata:
+  name: manager-config
+  namespace: default
+data:
+  config.yaml: |
+    ignore-missing-collector-crds: true
+    enable-instrumentation-crds: false
+    enable-multi-instrumentation: false
+    instrumentations:
+      java:
+        exporter:
+          endpoint: http://collector.default.svc:4318
+        propagators:
+          - tracecontext
+          - baggage
+          - b3
+        java:
+          image: "java-autoinstrumentation:dev"
+---
+apiVersion: apps/v1
+kind: Deployment
+metadata:
+  name: operator
+spec:
+  replicas: 1
+  selector:
+    matchLabels:
+      app: operator
+  template:
+    metadata:
+      name: operator
+      labels:
+        app: operator
+    spec:
+      serviceAccountName: operator
+      containers:
+        - image: manager:dev
+          name: operator
+          imagePullPolicy: IfNotPresent
+          env:
+            - name: KUBERNETES_MASTER
+              value: kube-apiserver-kind-control-plane
+          ports:
+            - containerPort: 9443
+              name: webhook-server
+          volumeMounts:
+            - mountPath: /tmp/k8s-webhook-server/serving-certs
+              name: certs
+            - mountPath: /etc/config.yaml
+              name: config
+              subPath: config.yaml
+          command:
+            - /manager
+            - --config-file
+            - /etc/config.yaml
+      volumes:
+        - name: certs
+          configMap:
+            name: certs
+        - name: config
+          configMap:
+            name: manager-config
+---
+apiVersion: rbac.authorization.k8s.io/v1
+kind: ClusterRole
+metadata:
+  name: operator
+rules:
+  - apiGroups: [""]
+    resources:
+      - configmaps
+      - persistentvolumeclaims
+      - persistentvolumes
+      - pods
+      - serviceaccounts
+      - services
+      - namespaces
+    verbs: ["get", "watch", "list"]
+  - apiGroups: [ "" ]
+    resources:
+      - events
+    verbs: [ "get", "watch", "list", "create", "patch" ]
+  - apiGroups: ["apps", "extensions"]
+    resources:
+      - daemonsets
+      - deployments
+      - statefulsets
+      - replicasets
+    verbs: ["get", "watch", "list"]
+  - apiGroups: [ "autoscaling" ]
+    resources:
+      - horizontalpodautoscalers
+    verbs: [ "get", "watch", "list" ]
+  - apiGroups: [ "policy" ]
+    resources:
+      - poddisruptionbudgets
+    verbs: [ "get", "watch", "list" ]
+  - apiGroups: ["networking.k8s.io"]
+    resources:
+      - ingresses
+    verbs: [ "get", "watch", "list" ]
+---
+apiVersion: v1
+kind: ServiceAccount
+metadata:
+  name: operator
+---
+apiVersion: rbac.authorization.k8s.io/v1
+kind: ClusterRoleBinding
+metadata:
+  name: watch-deployments
+roleRef:
+  kind: ClusterRole
+  name: operator
+  apiGroup: rbac.authorization.k8s.io
+subjects:
+  - kind: ServiceAccount
+    name: operator
+    namespace: default
+---
+apiVersion: v1
+kind: Service
+metadata:
+  name: operator-webhook
+  namespace: default
+spec:
+  ports:
+    - port: 443
+      protocol: TCP
+      targetPort: webhook-server
+  selector:
+    app: operator
+---
+apiVersion: admissionregistration.k8s.io/v1
+kind: MutatingWebhookConfiguration
+metadata:
+  labels:
+    app.kubernetes.io/component: webhook
+  name: webhook-mutation
+webhooks:
+  - admissionReviewVersions:
+      - v1
+    clientConfig:
+      caBundle: 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
+      service:
+        name: operator-webhook
+        namespace: default
+        path: /mutate-v1-pod
+        port: 443
+    failurePolicy: Ignore
+    name: mpod.kb.io
+    rules:
+      - apiGroups:
+          - ""
+        apiVersions:
+          - v1
+        operations:
+          - CREATE
+        resources:
+          - pods
+        scope: Namespaced
+    sideEffects: None
+    timeoutSeconds: 30
\ No newline at end of file