diff --git a/test/e2e/deployment_test.go b/test/e2e/deployment_test.go
index bb12e5efbbd9f..dee795f8facae 100644
--- a/test/e2e/deployment_test.go
+++ b/test/e2e/deployment_test.go
@@ -1,12 +1,18 @@
 package e2e
 
 import (
+	"fmt"
 	"testing"
 
+	"github.com/stretchr/testify/assert"
+
+	"github.com/argoproj/argo-cd/v2/util/argo"
+
 	"github.com/argoproj/gitops-engine/pkg/health"
 	. "github.com/argoproj/gitops-engine/pkg/sync/common"
 
 	. "github.com/argoproj/argo-cd/v2/pkg/apis/application/v1alpha1"
+	. "github.com/argoproj/argo-cd/v2/test/e2e/fixture"
 	. "github.com/argoproj/argo-cd/v2/test/e2e/fixture/app"
 )
 
@@ -31,3 +37,70 @@ func TestDeployment(t *testing.T) {
 ]`).
 		Sync()
 }
+
+func TestDeploymentWithAnnotationTrackingMode(t *testing.T) {
+	ctx := Given(t)
+
+	SetTrackingMethod(string(argo.TrackingMethodAnnotation))
+	ctx.
+		Path("deployment").
+		When().
+		Create().
+		Sync().
+		Then().
+		Expect(OperationPhaseIs(OperationSucceeded)).
+		Expect(SyncStatusIs(SyncStatusCodeSynced)).
+		Expect(HealthIs(health.HealthStatusHealthy)).
+		When().
+		Then().
+		And(func(app *Application) {
+			out, err := RunCli("app", "manifests", app.Name)
+			assert.NoError(t, err)
+			assert.Contains(t, out, fmt.Sprintf(`annotations:
+    app.kubernetes.io/instance: %s`, Name()))
+		})
+}
+
+func TestDeploymentWithLabelTrackingMode(t *testing.T) {
+	ctx := Given(t)
+	SetTrackingMethod(string(argo.TrackingMethodLabel))
+	ctx.
+		Path("deployment").
+		When().
+		Create().
+		Sync().
+		Then().
+		Expect(OperationPhaseIs(OperationSucceeded)).
+		Expect(SyncStatusIs(SyncStatusCodeSynced)).
+		Expect(HealthIs(health.HealthStatusHealthy)).
+		When().
+		Then().
+		And(func(app *Application) {
+			out, err := RunCli("app", "manifests", app.Name)
+			assert.NoError(t, err)
+			assert.Contains(t, out, fmt.Sprintf(`labels:
+    app: nginx
+    app.kubernetes.io/instance: %s`, Name()))
+		})
+}
+
+func TestDeploymentWithoutTrackingMode(t *testing.T) {
+	Given(t).
+		Path("deployment").
+		When().
+		Create().
+		Sync().
+		Then().
+		Expect(OperationPhaseIs(OperationSucceeded)).
+		Expect(SyncStatusIs(SyncStatusCodeSynced)).
+		Expect(HealthIs(health.HealthStatusHealthy)).
+		When().
+		Then().
+		And(func(app *Application) {
+			out, err := RunCli("app", "manifests", app.Name)
+			assert.NoError(t, err)
+			assert.Contains(t, out, fmt.Sprintf(`labels:
+    app: nginx
+    app.kubernetes.io/instance: %s`, Name()))
+		})
+}
diff --git a/test/e2e/fixture/fixture.go b/test/e2e/fixture/fixture.go
index 08d0f16d9919f..95789cdbed710 100644
--- a/test/e2e/fixture/fixture.go
+++ b/test/e2e/fixture/fixture.go
@@ -336,6 +336,13 @@ func SetResourceOverrides(overrides map[string]v1alpha1.ResourceOverride) {
 	SetResourceOverridesSplitKeys(overrides)
 }
 
+func SetTrackingMethod(trackingMethod string) {
+	updateSettingConfigMap(func(cm *corev1.ConfigMap) error {
+		cm.Data["application.resourceTrackingMethod"] = trackingMethod
+		return nil
+	})
+}
+
 func SetResourceOverridesSplitKeys(overrides map[string]v1alpha1.ResourceOverride) {
 	updateSettingConfigMap(func(cm *corev1.ConfigMap) error {
 		for k, v := range overrides {