diff --git a/pkg/kapp/app/recorded_app.go b/pkg/kapp/app/recorded_app.go
index 368526aa1..2ec334e44 100644
--- a/pkg/kapp/app/recorded_app.go
+++ b/pkg/kapp/app/recorded_app.go
@@ -105,8 +105,13 @@ func (a *RecordedApp) UpdateUsedGVsAndGKs(gvs []schema.GroupVersion, gks []schem
 		}
 	}
 
+	sort.Slice(uniqGVs, func(i int, j int) bool {
+		return uniqGVs[i].Group+uniqGVs[i].Version < uniqGVs[j].Group+uniqGVs[j].Version
+	})
+
 	gksByGK := map[schema.GroupKind]struct{}{}
-	var uniqGKs []schema.GroupKind
+	// Initialize with an empty slice so that we do not remove `usedGKs` from meta configmap
+	uniqGKs := []schema.GroupKind{} 
 
 	for _, gk := range gks {
 		if _, found := gksByGK[gk]; !found {
@@ -115,10 +120,6 @@ func (a *RecordedApp) UpdateUsedGVsAndGKs(gvs []schema.GroupVersion, gks []schem
 		}
 	}
 
-	sort.Slice(uniqGVs, func(i int, j int) bool {
-		return uniqGVs[i].Group+uniqGVs[i].Version < uniqGVs[j].Group+uniqGVs[j].Version
-	})
-
 	sort.Slice(uniqGKs, func(i int, j int) bool {
 		return uniqGKs[i].Group+uniqGKs[i].Kind < uniqGKs[j].Group+uniqGKs[j].Kind
 	})
diff --git a/test/e2e/app_metadata_output_test.go b/test/e2e/app_metadata_output_test.go
index 61405cacb..b0e0368c2 100644
--- a/test/e2e/app_metadata_output_test.go
+++ b/test/e2e/app_metadata_output_test.go
@@ -55,10 +55,18 @@ metadata:
 	assert.NoError(t, err)
 	thirdDeploy, err := os.CreateTemp(os.TempDir(), "output3")
 	assert.NoError(t, err)
+	fourthDeploy, err := os.CreateTemp(os.TempDir(), "output4")
+	assert.NoError(t, err)
+
+	tmpDir, err := os.MkdirTemp("", "")
+	assert.NoError(t, err)
+	defer os.RemoveAll(tmpDir)
 
 	defer func() {
 		os.Remove(firstDeploy.Name())
 		os.Remove(secondDeploy.Name())
+		os.Remove(thirdDeploy.Name())
+		os.Remove(fourthDeploy.Name())
 	}()
 
 	logger.Section("deploy app", func() {
@@ -73,6 +81,10 @@ metadata:
 		kapp.RunWithOpts([]string{"deploy", "--app-metadata-file-output", thirdDeploy.Name(), "-f", "-", "-a", name}, RunOpts{IntoNs: true, StdinReader: strings.NewReader(yaml2)})
 	})
 
+	logger.Section("deploy with no changes", func() {
+		kapp.RunWithOpts([]string{"deploy", "--app-metadata-file-output", fourthDeploy.Name(), "-f", tmpDir, "-a", name, "--dangerous-allow-empty-list-of-resources"}, RunOpts{IntoNs: true})
+	})
+
 	configMapFirstDeploy, err := os.ReadFile(firstDeploy.Name())
 	assert.NoError(t, err)
 
@@ -93,4 +105,11 @@ metadata:
 	thirdConfigMap := yamlSubset{}
 	require.NoError(t, yaml.Unmarshal(configMapThirdDeploy, &thirdConfigMap))
 	require.Equal(t, yamlSubset{LastChange: lastChange{Namespaces: []string{env.Namespace}}, UsedGKs: []usedGK{{Group: "", Kind: "Secret"}}}, thirdConfigMap)
+
+	configMapFourthDeploy, err := os.ReadFile(fourthDeploy.Name())
+	assert.NoError(t, err)
+
+	fourthConfigMap := yamlSubset{}
+	require.NoError(t, yaml.Unmarshal(configMapFourthDeploy, &fourthConfigMap))
+	require.Equal(t, yamlSubset{LastChange: lastChange{Namespaces: nil}, UsedGKs: []usedGK{}}, fourthConfigMap)
 }