diff --git a/pkg/autodetect/main.go b/pkg/autodetect/main.go
index 296baa4a2..590c75c2b 100644
--- a/pkg/autodetect/main.go
+++ b/pkg/autodetect/main.go
@@ -243,7 +243,7 @@ func (b *Background) cleanDeployments(ctx context.Context) {
 
 	// check deployments to see which one needs to be cleaned.
 	for _, dep := range deployments.Items {
-		if instanceName, ok := dep.Annotations[inject.Annotation]; ok {
+		if instanceName, ok := dep.Labels[inject.Label]; ok {
 			_, instanceExists := instancesMap[instanceName]
 			if !instanceExists { // Jaeger instance not exist anymore, we need to clean this up.
 				inject.CleanSidecar(&dep)
diff --git a/pkg/inject/sidecar.go b/pkg/inject/sidecar.go
index 541d171f9..eed1535df 100644
--- a/pkg/inject/sidecar.go
+++ b/pkg/inject/sidecar.go
@@ -43,20 +43,25 @@ func Sidecar(jaeger *v1.Jaeger, dep *appsv1.Deployment) *appsv1.Deployment {
 	deployment.NewAgent(jaeger) // we need some initialization from that, but we don't actually need the agent's instance here
 	logFields := jaeger.Logger().WithField("deployment", dep.Name)
 
-	if jaeger == nil || (dep.Annotations[Annotation] != jaeger.Name && dep.Annotations[AnnotationLegacy] != jaeger.Name) {
-		logFields.Trace("skipping sidecar injection")
-	} else {
-		decorate(dep)
+	if jaeger == nil {
+		logFields.Trace("no Jaeger instance found, skipping sidecar injection")
+		return dep
+	}
 
-		logFields.Debug("injecting sidecar")
-		dep.Spec.Template.Spec.Containers = append(dep.Spec.Template.Spec.Containers, container(jaeger, dep))
+	if val, ok := dep.Labels[Label]; ok && val != jaeger.Name {
+		logFields.Trace("deployment is assigned to a different Jaeger instance, skipping sidecar injection")
+		return dep
+	}
 
-		jaegerName := util.Truncate(jaeger.Name, 63)
-		if dep.Labels == nil {
-			dep.Labels = map[string]string{Label: jaegerName}
-		} else {
-			dep.Labels[Label] = jaegerName
-		}
+	decorate(dep)
+	logFields.Debug("injecting sidecar")
+	dep.Spec.Template.Spec.Containers = append(dep.Spec.Template.Spec.Containers, container(jaeger, dep))
+	jaegerName := util.Truncate(jaeger.Name, 63)
+
+	if dep.Labels == nil {
+		dep.Labels = map[string]string{Label: jaegerName}
+	} else {
+		dep.Labels[Label] = jaegerName
 	}
 
 	return dep
@@ -104,10 +109,6 @@ func Select(target *appsv1.Deployment, ns *corev1.Namespace, availableJaegerPods
 		// jaeger instance to use!
 		// first, we make sure we normalize the name:
 		jaeger := &availableJaegerPods.Items[0]
-		if target.Annotations == nil {
-			target.Annotations = map[string]string{}
-		}
-		target.Annotations[Annotation] = jaeger.Name
 		return jaeger
 	}
 	return nil
diff --git a/pkg/inject/sidecar_test.go b/pkg/inject/sidecar_test.go
index 8b32948b6..9cf9f0257 100644
--- a/pkg/inject/sidecar_test.go
+++ b/pkg/inject/sidecar_test.go
@@ -32,17 +32,9 @@ func reset() {
 
 func TestInjectSidecar(t *testing.T) {
 	jaeger := v1.NewJaeger(types.NamespacedName{Name: "TestInjectSidecar"})
-	dep := dep(map[string]string{Annotation: jaeger.Name}, map[string]string{})
-	dep = Sidecar(jaeger, dep)
-	assert.Len(t, dep.Spec.Template.Spec.Containers, 2)
-	assert.Contains(t, dep.Spec.Template.Spec.Containers[1].Image, "jaeger-agent")
-	assert.Len(t, dep.Spec.Template.Spec.Containers[0].Env, 0)
-}
-
-func TestInjectSidecarWithLegacyAnnotation(t *testing.T) {
-	jaeger := v1.NewJaeger(types.NamespacedName{Name: "TestInjectSidecarWithLegacyAnnotation"})
-	dep := dep(map[string]string{AnnotationLegacy: jaeger.Name}, map[string]string{})
+	dep := dep(map[string]string{}, map[string]string{})
 	dep = Sidecar(jaeger, dep)
+	assert.Equal(t, dep.Labels[Label], jaeger.Name)
 	assert.Len(t, dep.Spec.Template.Spec.Containers, 2)
 	assert.Contains(t, dep.Spec.Template.Spec.Containers[1].Image, "jaeger-agent")
 	assert.Len(t, dep.Spec.Template.Spec.Containers[0].Env, 0)
@@ -70,7 +62,7 @@ func TestInjectSidecarWithEnvVars(t *testing.T) {
 func TestInjectSidecarWithEnvVarsK8sAppName(t *testing.T) {
 	// prepare
 	jaeger := v1.NewJaeger(types.NamespacedName{Name: "TestInjectSidecarWithEnvVarsK8sAppName"})
-	dep := dep(map[string]string{Annotation: jaeger.Name}, map[string]string{
+	dep := dep(map[string]string{}, map[string]string{
 		"app":                    "noapp",
 		"app.kubernetes.io/name": "testapp",
 	})
@@ -87,7 +79,7 @@ func TestInjectSidecarWithEnvVarsK8sAppName(t *testing.T) {
 func TestInjectSidecarWithEnvVarsK8sAppInstance(t *testing.T) {
 	// prepare
 	jaeger := v1.NewJaeger(types.NamespacedName{Name: "TestInjectSidecarWithEnvVarsK8sAppInstance"})
-	dep := dep(map[string]string{Annotation: jaeger.Name}, map[string]string{
+	dep := dep(map[string]string{}, map[string]string{
 		"app":                        "noapp",
 		"app.kubernetes.io/name":     "noname",
 		"app.kubernetes.io/instance": "testapp",
@@ -105,7 +97,7 @@ func TestInjectSidecarWithEnvVarsK8sAppInstance(t *testing.T) {
 func TestInjectSidecarWithEnvVarsWithNamespace(t *testing.T) {
 	// prepare
 	jaeger := v1.NewJaeger(types.NamespacedName{Name: "TestInjectSidecarWithEnvVarsWithNamespace"})
-	dep := dep(map[string]string{Annotation: jaeger.Name}, map[string]string{"app": "testapp"})
+	dep := dep(map[string]string{}, map[string]string{"app": "testapp"})
 	dep.Namespace = "mynamespace"
 
 	// test
@@ -123,7 +115,7 @@ func TestInjectSidecarWithEnvVarsWithNamespace(t *testing.T) {
 func TestInjectSidecarWithEnvVarsOverrideName(t *testing.T) {
 	// prepare
 	jaeger := v1.NewJaeger(types.NamespacedName{Name: "TestInjectSidecarWithEnvVarsOverrideName"})
-	dep := dep(map[string]string{Annotation: jaeger.Name}, map[string]string{"app": "testapp"})
+	dep := dep(map[string]string{}, map[string]string{"app": "testapp"})
 	envVar := corev1.EnvVar{
 		Name:  envVarServiceName,
 		Value: "otherapp",
@@ -149,7 +141,7 @@ func TestInjectSidecarWithEnvVarsOverridePropagation(t *testing.T) {
 		Name:  envVarPropagation,
 		Value: "tracecontext",
 	}
-	dep := dep(map[string]string{Annotation: jaeger.Name}, map[string]string{"app": "testapp"})
+	dep := dep(map[string]string{}, map[string]string{"app": "testapp"})
 	dep.Spec.Template.Spec.Containers[0].Env = append(dep.Spec.Template.Spec.Containers[0].Env, traceContextEnvVar)
 
 	// test
@@ -167,7 +159,7 @@ func TestInjectSidecarWithEnvVarsOverridePropagation(t *testing.T) {
 func TestSidecarDefaultPorts(t *testing.T) {
 	// prepare
 	jaeger := v1.NewJaeger(types.NamespacedName{Name: "TestSidecarPorts"})
-	dep := dep(map[string]string{Annotation: jaeger.Name}, map[string]string{"app": "testapp"})
+	dep := dep(map[string]string{}, map[string]string{"app": "testapp"})
 
 	// test
 	dep = Sidecar(jaeger, dep)
@@ -187,7 +179,7 @@ func TestSidecarDefaultPorts(t *testing.T) {
 func TestSkipInjectSidecar(t *testing.T) {
 	// prepare
 	jaeger := v1.NewJaeger(types.NamespacedName{Name: "TestSkipInjectSidecar"})
-	dep := dep(map[string]string{Annotation: "non-existing-operator"}, map[string]string{})
+	dep := dep(map[string]string{}, map[string]string{Label: "non-existing-operator"})
 
 	// test
 	dep = Sidecar(jaeger, dep)
@@ -198,7 +190,7 @@ func TestSkipInjectSidecar(t *testing.T) {
 }
 
 func TestSidecarNeeded(t *testing.T) {
-	depWithAgent := dep(map[string]string{Annotation: "some-jaeger-instance"}, map[string]string{})
+	depWithAgent := dep(map[string]string{}, map[string]string{})
 	depWithAgent.Spec.Template.Spec.Containers = append(depWithAgent.Spec.Template.Spec.Containers, corev1.Container{
 		Name: "jaeger-agent",
 	})
@@ -375,7 +367,7 @@ func TestSidecarOrderOfArguments(t *testing.T) {
 		"c-option": "c-value",
 	})
 
-	dep := dep(map[string]string{Annotation: jaeger.Name}, map[string]string{})
+	dep := dep(map[string]string{}, map[string]string{})
 	dep = Sidecar(jaeger, dep)
 
 	assert.Len(t, dep.Spec.Template.Spec.Containers, 2)
@@ -394,7 +386,7 @@ func TestSidecarExplicitTags(t *testing.T) {
 	// prepare
 	jaeger := v1.NewJaeger(types.NamespacedName{Name: "TestSidecarExplicitTags"})
 	jaeger.Spec.Agent.Options = v1.NewOptions(map[string]interface{}{"jaeger.tags": "key=val"})
-	dep := dep(map[string]string{Annotation: jaeger.Name}, map[string]string{})
+	dep := dep(map[string]string{}, map[string]string{})
 
 	// test
 	dep = Sidecar(jaeger, dep)
@@ -412,7 +404,7 @@ func TestSidecarOverrideReporter(t *testing.T) {
 		"reporter.thrift.host-port": "collector:14267",
 	})
 
-	dep := dep(map[string]string{Annotation: jaeger.Name}, map[string]string{})
+	dep := dep(map[string]string{}, map[string]string{})
 	dep = Sidecar(jaeger, dep)
 
 	assert.Len(t, dep.Spec.Template.Spec.Containers, 2)
@@ -444,7 +436,7 @@ func TestSidecarAgentResources(t *testing.T) {
 		},
 	}
 
-	dep := dep(map[string]string{Annotation: jaeger.Name}, map[string]string{})
+	dep := dep(map[string]string{}, map[string]string{})
 	dep = Sidecar(jaeger, dep)
 
 	assert.Len(t, dep.Spec.Template.Spec.Containers, 2, "Expected 2 containers")
@@ -463,7 +455,7 @@ func TestCleanSidecars(t *testing.T) {
 		Namespace: "Test",
 	}
 	jaeger := v1.NewJaeger(nsn)
-	dep1 := Sidecar(jaeger, dep(map[string]string{Annotation: jaeger.Name}, map[string]string{}))
+	dep1 := Sidecar(jaeger, dep(map[string]string{}, map[string]string{}))
 	CleanSidecar(dep1)
 	assert.Equal(t, len(dep1.Spec.Template.Spec.Containers), 1)
 
@@ -475,10 +467,10 @@ func TestSidecarWithLabel(t *testing.T) {
 		Namespace: "Test",
 	}
 	jaeger := v1.NewJaeger(nsn)
-	dep1 := dep(map[string]string{Annotation: jaeger.Name}, map[string]string{})
+	dep1 := dep(map[string]string{}, map[string]string{})
 	dep1 = Sidecar(jaeger, dep1)
 	assert.Equal(t, dep1.Labels[Label], "TestSidecarWithLabel")
-	dep2 := dep(map[string]string{Annotation: jaeger.Name}, map[string]string{})
+	dep2 := dep(map[string]string{}, map[string]string{})
 	dep2.Labels = map[string]string{"anotherLabel": "anotherValue"}
 	dep2 = Sidecar(jaeger, dep2)
 	assert.Equal(t, len(dep2.Labels), 2)
@@ -489,7 +481,7 @@ func TestSidecarWithLabel(t *testing.T) {
 func TestSidecarWithoutPrometheusAnnotations(t *testing.T) {
 	// prepare
 	jaeger := v1.NewJaeger(types.NamespacedName{Name: "TestSidecarWithoutPrometheusAnnotations"})
-	dep := Sidecar(jaeger, dep(map[string]string{Annotation: jaeger.Name}, map[string]string{}))
+	dep := Sidecar(jaeger, dep(map[string]string{}, map[string]string{}))
 
 	// test
 	dep = Sidecar(jaeger, dep)
@@ -503,7 +495,6 @@ func TestSidecarWithPrometheusAnnotations(t *testing.T) {
 	// prepare
 	jaeger := v1.NewJaeger(types.NamespacedName{Name: "TestSidecarWithPrometheusAnnotations"})
 	dep := dep(map[string]string{
-		Annotation:             jaeger.Name,
 		"prometheus.io/scrape": "false",
 		"prometheus.io/port":   "9090",
 	}, map[string]string{})
@@ -518,8 +509,9 @@ func TestSidecarWithPrometheusAnnotations(t *testing.T) {
 
 func TestSidecarAgentTagsWithMultipleContainers(t *testing.T) {
 	jaeger := v1.NewJaeger(types.NamespacedName{Name: "TestSidecarAgentTagsWithMultipleContainers"})
-	dep := Sidecar(jaeger, depWithTwoContainers(map[string]string{Annotation: jaeger.Name}, map[string]string{}))
+	dep := Sidecar(jaeger, depWithTwoContainers(map[string]string{}, map[string]string{}))
 
+	assert.Equal(t, dep.Labels[Label], jaeger.Name)
 	assert.Len(t, dep.Spec.Template.Spec.Containers, 3, "Expected 3 containers")
 	assert.Equal(t, "jaeger-agent", dep.Spec.Template.Spec.Containers[2].Name)
 	containsOptionWithPrefix(t, dep.Spec.Template.Spec.Containers[2].Args, "--jaeger.tags")
diff --git a/test/e2e/sidecar_test.go b/test/e2e/sidecar_test.go
index 2b690cc8f..eafb7d83c 100644
--- a/test/e2e/sidecar_test.go
+++ b/test/e2e/sidecar_test.go
@@ -16,6 +16,7 @@ import (
 	appsv1 "k8s.io/api/apps/v1"
 	corev1 "k8s.io/api/core/v1"
 	metav1 "k8s.io/apimachinery/pkg/apis/meta/v1"
+	"k8s.io/apimachinery/pkg/types"
 	"k8s.io/apimachinery/pkg/util/intstr"
 	"k8s.io/apimachinery/pkg/util/wait"
 
@@ -64,13 +65,14 @@ func (suite *SidecarTestSuite) AfterTest(suiteName, testName string) {
 
 // Sidecar runs a test with the agent as sidecar
 func (suite *SidecarTestSuite) TestSidecar() {
+
 	cleanupOptions := &framework.CleanupOptions{TestContext: ctx, Timeout: timeout, RetryInterval: retryInterval}
 
 	jaegerInstanceName := "agent-as-sidecar"
 	j := getJaegerAgentAsSidecarDefinition(jaegerInstanceName, namespace)
+	undeployJaegerInstance(j)
 	err := fw.Client.Create(goctx.TODO(), j, cleanupOptions)
 	require.NoError(t, err, "Failed to create jaeger instance")
-	defer undeployJaegerInstance(j)
 
 	err = e2eutil.WaitForDeployment(t, fw.KubeClient, namespace, jaegerInstanceName, 1, retryInterval, timeout)
 	require.NoError(t, err, "Error waiting for Jaeger instance deployment")
@@ -99,6 +101,45 @@ func (suite *SidecarTestSuite) TestSidecar() {
 		return len(resp.Data) > 0, nil
 	})
 	require.NoError(t, err, "Failed waiting for expected content")
+
+	/* Testing other instance */
+
+	otherJaegerInstanceName := "agent-as-sidecar2"
+	j2 := getJaegerAgentAsSidecarDefinition(otherJaegerInstanceName, namespace)
+	defer undeployJaegerInstance(j2)
+
+	err = fw.Client.Create(goctx.TODO(), j2, cleanupOptions)
+	err = e2eutil.WaitForDeployment(t, fw.KubeClient, namespace, jaegerInstanceName, 1, retryInterval, timeout)
+	require.NoError(t, err, "Error waiting for Jaeger instance deployment")
+
+	persisted := &appsv1.Deployment{}
+	err = fw.Client.Get(goctx.TODO(), types.NamespacedName{
+		Name:      "vertx-create-span-sidecar",
+		Namespace: namespace,
+	}, persisted)
+	require.NoError(t, err, "Error getting jaeger instance")
+	require.Equal(t, "agent-as-sidecar", persisted.Labels[inject.Label])
+
+	err = fw.Client.Delete(goctx.TODO(), j)
+	require.NoError(t, err, "Error deleting instance")
+
+	url, httpClient = getQueryURLAndHTTPClient(otherJaegerInstanceName, "%s/api/traces?service=order", true)
+	req, err = http.NewRequest(http.MethodGet, url, nil)
+
+	err = wait.Poll(retryInterval, timeout, func() (done bool, err error) {
+		res, err := httpClient.Do(req)
+		require.NoError(t, err)
+
+		body, err := ioutil.ReadAll(res.Body)
+		require.NoError(t, err)
+
+		resp := &resp{}
+		err = json.Unmarshal(body, &resp)
+		require.NoError(t, err)
+
+		return len(resp.Data) > 0, nil
+	})
+	require.NoError(t, err, "Failed waiting for expected content")
 }
 
 func getVertxDefinition(annotations map[string]string) *appsv1.Deployment {
diff --git a/test/e2e/utils.go b/test/e2e/utils.go
index c432ad468..1f465a1d9 100644
--- a/test/e2e/utils.go
+++ b/test/e2e/utils.go
@@ -243,13 +243,20 @@ func printTestStackTrace() {
 	}
 }
 
-func undeployJaegerInstance(jaeger *v1.Jaeger) {
+func undeployJaegerInstance(jaeger *v1.Jaeger) bool {
 	if !debugMode || !t.Failed() {
 		err := fw.Client.Delete(goctx.TODO(), jaeger)
-		require.NoError(t, err, "Error undeploying Jaeger")
-		err = e2eutil.WaitForDeletion(t, fw.Client.Client, jaeger, retryInterval, timeout)
-		require.NoError(t, err)
+		if err := fw.Client.Delete(goctx.TODO(), jaeger); err != nil {
+			return false
+		}
+
+		if err = e2eutil.WaitForDeletion(t, fw.Client.Client, jaeger, retryInterval, timeout); err != nil {
+			return false
+		}
+		return true
 	}
+	// Always return true, we don't care
+	return true
 }
 
 func getJaegerInstance(name, namespace string) *v1.Jaeger {