diff --git a/pkg/fargate/coredns/coredns.go b/pkg/fargate/coredns/coredns.go
index b451161102..8c4b89fa4d 100644
--- a/pkg/fargate/coredns/coredns.go
+++ b/pkg/fargate/coredns/coredns.go
@@ -67,7 +67,7 @@ func isDeploymentScheduledOnFargate(clientSet kubeclient.Interface) (bool, error
 	if coredns.Spec.Replicas == nil {
 		return false, errors.New("nil spec.replicas in coredns deployment")
 	}
-	computeType, exists := coredns.Spec.Template.Annotations[ComputeTypeAnnotationKey]
+	computeType, exists := safeGetAnnotationValue(coredns.Spec.Template.Annotations, ComputeTypeAnnotationKey)
 	logger.Debug("deployment %q with compute type %q currently has %v/%v replicas running", Name, computeType, coredns.Status.ReadyReplicas, *coredns.Spec.Replicas)
 	scheduled := exists &&
 		computeType == computeTypeFargate &&
@@ -95,7 +95,7 @@ func arePodsScheduledOnFargate(clientSet kubeclient.Interface) (bool, error) {
 }
 
 func isRunningOnFargate(pod *v1.Pod) bool {
-	computeType, exists := pod.Annotations[ComputeTypeAnnotationKey]
+	computeType, exists := safeGetAnnotationValue(pod.Annotations, ComputeTypeAnnotationKey)
 	logger.Debug("pod %q with compute type %q and status %q is scheduled on %q", pod.Name, computeType, pod.Status.Phase, pod.Spec.NodeName)
 	return exists &&
 		computeType == computeTypeFargate &&
@@ -119,7 +119,7 @@ func scheduleOnFargate(clientSet kubeclient.Interface) error {
 	if err != nil {
 		return err
 	}
-	coredns.Spec.Template.Annotations[ComputeTypeAnnotationKey] = computeTypeFargate
+	coredns.Spec.Template.Annotations = safeSetAnnotation(coredns.Spec.Template.Annotations, ComputeTypeAnnotationKey, computeTypeFargate)
 	bytes, err := runtime.Encode(unstructured.UnstructuredJSONScheme, coredns)
 	if err != nil {
 		return errors.Wrapf(err, "failed to marshal %q deployment", Name)
@@ -128,7 +128,8 @@ func scheduleOnFargate(clientSet kubeclient.Interface) error {
 	if err != nil {
 		return errors.Wrap(err, "failed to patch deployment")
 	}
-	value, exists := patched.Spec.Template.Annotations[ComputeTypeAnnotationKey]
+
+	value, exists := safeGetAnnotationValue(patched.Spec.Template.Annotations, ComputeTypeAnnotationKey)
 	if !exists {
 		return fmt.Errorf("could not find annotation %q on patched deployment %q: patching must have failed", ComputeTypeAnnotationKey, Name)
 	}
@@ -156,3 +157,23 @@ func WaitForScheduleOnFargate(clientSet kubeclient.Interface, retryPolicy retry.
 	}
 	return fmt.Errorf("timed out while waiting for %q to be scheduled on Fargate", Name)
 }
+
+// safeGetAnnotationValue safely gets the value of an annotation from a map. It
+// returns the value and a boolean indicating whether the key was found.
+func safeGetAnnotationValue(annotations map[string]string, key string) (string, bool) {
+	if annotations == nil {
+		return "", false
+	}
+	value, exist := annotations[key]
+	return value, exist
+}
+
+// safeSetAnnotation safely sets the value of an annotation in a map. It will
+// initialize the annotaions map if it is nil.
+func safeSetAnnotation(annotations map[string]string, key, value string) map[string]string {
+	if annotations == nil {
+		annotations = make(map[string]string)
+	}
+	annotations[key] = value
+	return annotations
+}
diff --git a/pkg/fargate/coredns/coredns_test.go b/pkg/fargate/coredns/coredns_test.go
index 4b5c7e2d2e..f2a93df1a0 100644
--- a/pkg/fargate/coredns/coredns_test.go
+++ b/pkg/fargate/coredns/coredns_test.go
@@ -122,6 +122,7 @@ var _ = Describe("coredns", func() {
 			mockClientset := mockClientsetWith(deployment("ec2", 0, 2))
 			deployment, err := mockClientset.AppsV1().Deployments(coredns.Namespace).Get(context.Background(), coredns.Name, metav1.GetOptions{})
 			Expect(err).To(Not(HaveOccurred()))
+			Expect(deployment.Spec.Template.Annotations).NotTo(BeNil())
 			Expect(deployment.Spec.Template.Annotations).To(HaveKeyWithValue(coredns.ComputeTypeAnnotationKey, "ec2"))
 			// When:
 			err = coredns.ScheduleOnFargate(mockClientset)
@@ -129,11 +130,23 @@ var _ = Describe("coredns", func() {
 			// Then:
 			deployment, err = mockClientset.AppsV1().Deployments(coredns.Namespace).Get(context.Background(), coredns.Name, metav1.GetOptions{})
 			Expect(err).To(Not(HaveOccurred()))
+			Expect(deployment.Spec.Template.Annotations).NotTo(BeNil())
 			Expect(deployment.Spec.Template.Annotations).To(HaveKeyWithValue(coredns.ComputeTypeAnnotationKey, "fargate"))
 		})
 	})
 
 	Describe("WaitForScheduleOnFargate", func() {
+		It("should error if the annotations are not set", func() {
+			// Given:
+			mockClientset := mockClientsetWith(
+				deployment("fargate", 2, 2), podWithAnnotations("fargate", v1.PodRunning, nil), pod("fargate", v1.PodRunning),
+			)
+			// When:
+			err := coredns.WaitForScheduleOnFargate(mockClientset, retryPolicy)
+			// Then:
+			Expect(err).To(HaveOccurred())
+		})
+
 		It("should wait for coredns to be scheduled on Fargate and return w/o any error", func() {
 			// Given:
 			mockClientset := mockClientsetWith(
@@ -149,6 +162,8 @@ var _ = Describe("coredns", func() {
 			failureCases := [][]runtime.Object{
 				{deployment("ec2", 2, 2), pod("ec2", v1.PodRunning), pod("ec2", v1.PodRunning)},
 				{deployment("ec2", 0, 2), pod("ec2", v1.PodPending), pod("ec2", v1.PodPending)},
+				{deploymentWithAnnotations("ec2", 0, 2, nil), podWithAnnotations("ec2", v1.PodFailed, nil), podWithAnnotations("ec2", v1.PodFailed, nil)},
+				{deploymentWithAnnotations("ec2", 0, 2, nil), podWithAnnotations("ec2", v1.PodFailed, map[string]string{}), podWithAnnotations("ec2", v1.PodFailed, map[string]string{})},
 				{deployment("fargate", 0, 2), pod("fargate", v1.PodPending), pod("fargate", v1.PodPending)},
 				{deployment("fargate", 0, 2), pod("fargate", v1.PodFailed), pod("fargate", v1.PodFailed)},
 				{deployment("fargate", 0, 2), pod("fargate", v1.PodPending), pod("fargate", v1.PodFailed)},
@@ -165,6 +180,22 @@ var _ = Describe("coredns", func() {
 				Expect(err.Error()).To(Equal("timed out while waiting for \"coredns\" to be scheduled on Fargate"))
 			}
 		})
+
+		It("Should timeout if coredns pods do not have the correct annotations", func() {
+			failureCases := [][]runtime.Object{
+				{deploymentWithAnnotations("fargate", 0, 2, nil), podWithAnnotations("fargate", v1.PodPending, nil), podWithAnnotations("fargate", v1.PodRunning, nil)},
+				{deploymentWithAnnotations("ec2", 0, 2, nil), podWithAnnotations("ec2", v1.PodFailed, nil), podWithAnnotations("ec2", v1.PodRunning, nil)},
+				{deploymentWithAnnotations("ec2", 0, 2, map[string]string{}), podWithAnnotations("ec2", v1.PodRunning, map[string]string{}), podWithAnnotations("ec2", v1.PodRunning, map[string]string{})},
+			}
+			for _, failureCase := range failureCases {
+				// Given:
+				mockClientset := mockClientsetWith(failureCase...)
+				// When:
+				err := coredns.WaitForScheduleOnFargate(mockClientset, retryPolicy)
+				// Then:
+				Expect(err).To(MatchError("timed out while waiting for \"coredns\" to be scheduled on Fargate"))
+			}
+		})
 	})
 
 })
@@ -173,7 +204,7 @@ func mockClientsetWith(objects ...runtime.Object) kubeclient.Interface {
 	return fake.NewSimpleClientset(objects...)
 }
 
-func deployment(computeType string, numReady, numReplicas int32) *appsv1.Deployment {
+func deploymentWithAnnotations(computeType string, numReady, numReplicas int32, annotations map[string]string) *appsv1.Deployment {
 	return &appsv1.Deployment{
 		TypeMeta: metav1.TypeMeta{
 			Kind:       "Deployment",
@@ -187,9 +218,7 @@ func deployment(computeType string, numReady, numReplicas int32) *appsv1.Deploym
 			Replicas: &numReplicas,
 			Template: v1.PodTemplateSpec{
 				ObjectMeta: metav1.ObjectMeta{
-					Annotations: map[string]string{
-						coredns.ComputeTypeAnnotationKey: computeType,
-					},
+					Annotations: annotations,
 				},
 			},
 		},
@@ -199,9 +228,15 @@ func deployment(computeType string, numReady, numReplicas int32) *appsv1.Deploym
 	}
 }
 
+func deployment(computeType string, numReady, numReplicas int32) *appsv1.Deployment {
+	return deploymentWithAnnotations(computeType, numReady, numReplicas, map[string]string{
+		coredns.ComputeTypeAnnotationKey: computeType,
+	})
+}
+
 const chars = "abcdef0123456789"
 
-func pod(computeType string, phase v1.PodPhase) *v1.Pod {
+func podWithAnnotations(computeType string, phase v1.PodPhase, annotatations map[string]string) *v1.Pod {
 	pod := &v1.Pod{
 		TypeMeta: metav1.TypeMeta{
 			Kind:       "Pod",
@@ -213,9 +248,7 @@ func pod(computeType string, phase v1.PodPhase) *v1.Pod {
 			Labels: map[string]string{
 				"eks.amazonaws.com/component": coredns.Name,
 			},
-			Annotations: map[string]string{
-				coredns.ComputeTypeAnnotationKey: computeType,
-			},
+			Annotations: annotatations,
 		},
 		Status: v1.PodStatus{
 			Phase: phase,
@@ -230,3 +263,9 @@ func pod(computeType string, phase v1.PodPhase) *v1.Pod {
 	}
 	return pod
 }
+
+func pod(computeType string, phase v1.PodPhase) *v1.Pod {
+	return podWithAnnotations(computeType, phase, map[string]string{
+		coredns.ComputeTypeAnnotationKey: computeType,
+	})
+}