diff --git a/README.md b/README.md
index 6a10a962f3..bd7930ba42 100644
--- a/README.md
+++ b/README.md
@@ -215,6 +215,14 @@ The possible values for the annotation can be
 * `"my-instrumentation"` - name of `Instrumentation` CR instance.
 * `"false"` - do not inject
 
+It as also possible in case of multiple-containers Pods (like Istio sidecars) to specify the name of the container in which you want to inject OTEL auto-instrumentation (by default the first container is choosen)
+
+For this add this annotation to your Pod Specification with target container name :
+
+```bash
+instrumentation.opentelemetry.io/container-name: "name_of_your_target_container"
+```
+
 ## Compatibility matrix
 
 ### OpenTelemetry Operator vs. OpenTelemetry Collector
diff --git a/apis/v1alpha1/zz_generated.deepcopy.go b/apis/v1alpha1/zz_generated.deepcopy.go
index d21b1f660a..5ea87e5479 100644
--- a/apis/v1alpha1/zz_generated.deepcopy.go
+++ b/apis/v1alpha1/zz_generated.deepcopy.go
@@ -1,3 +1,4 @@
+//go:build !ignore_autogenerated
 // +build !ignore_autogenerated
 
 // Copyright The OpenTelemetry Authors
diff --git a/pkg/instrumentation/annotation.go b/pkg/instrumentation/annotation.go
index 8ce17a7c6f..c3036126f2 100644
--- a/pkg/instrumentation/annotation.go
+++ b/pkg/instrumentation/annotation.go
@@ -23,9 +23,10 @@ import (
 const (
 	// annotationInjectJava indicates whether java auto-instrumentation should be injected or not.
 	// Possible values are "true", "false" or "<Instrumentation>" name.
-	annotationInjectJava   = "instrumentation.opentelemetry.io/inject-java"
-	annotationInjectNodeJS = "instrumentation.opentelemetry.io/inject-nodejs"
-	annotationInjectPython = "instrumentation.opentelemetry.io/inject-python"
+	annotationInjectJava          = "instrumentation.opentelemetry.io/inject-java"
+	annotationInjectNodeJS        = "instrumentation.opentelemetry.io/inject-nodejs"
+	annotationInjectPython        = "instrumentation.opentelemetry.io/inject-python"
+	annotationInjectContainerName = "instrumentation.opentelemetry.io/container-name"
 )
 
 // annotationValue returns the effective annotationInjectJava value, based on the annotations from the pod and namespace.
diff --git a/pkg/instrumentation/javaagent.go b/pkg/instrumentation/javaagent.go
index aba5501100..8c935255c9 100644
--- a/pkg/instrumentation/javaagent.go
+++ b/pkg/instrumentation/javaagent.go
@@ -26,9 +26,9 @@ const (
 	javaJVMArgument     = " -javaagent:/otel-auto-instrumentation/javaagent.jar"
 )
 
-func injectJavaagent(logger logr.Logger, javaSpec v1alpha1.Java, pod corev1.Pod) corev1.Pod {
+func injectJavaagent(logger logr.Logger, javaSpec v1alpha1.Java, pod corev1.Pod, index int) corev1.Pod {
 	// caller checks if there is at least one container
-	container := &pod.Spec.Containers[0]
+	container := &pod.Spec.Containers[index]
 
 	// inject env vars
 	for _, env := range javaSpec.Env {
diff --git a/pkg/instrumentation/javaagent_test.go b/pkg/instrumentation/javaagent_test.go
index 28573d34fa..d97853bbfb 100644
--- a/pkg/instrumentation/javaagent_test.go
+++ b/pkg/instrumentation/javaagent_test.go
@@ -174,7 +174,7 @@ func TestInjectJavaagent(t *testing.T) {
 
 	for _, test := range tests {
 		t.Run(test.name, func(t *testing.T) {
-			pod := injectJavaagent(logr.Discard(), test.Java, test.pod)
+			pod := injectJavaagent(logr.Discard(), test.Java, test.pod, 0)
 			assert.Equal(t, test.expected, pod)
 		})
 	}
diff --git a/pkg/instrumentation/nodejs.go b/pkg/instrumentation/nodejs.go
index 810866a0af..7a893cf445 100644
--- a/pkg/instrumentation/nodejs.go
+++ b/pkg/instrumentation/nodejs.go
@@ -26,9 +26,9 @@ const (
 	nodeRequireArgument = " --require /otel-auto-instrumentation/autoinstrumentation.js"
 )
 
-func injectNodeJSSDK(logger logr.Logger, nodeJSSpec v1alpha1.NodeJS, pod corev1.Pod) corev1.Pod {
+func injectNodeJSSDK(logger logr.Logger, nodeJSSpec v1alpha1.NodeJS, pod corev1.Pod, index int) corev1.Pod {
 	// caller checks if there is at least one container
-	container := &pod.Spec.Containers[0]
+	container := &pod.Spec.Containers[index]
 
 	// inject env vars
 	for _, env := range nodeJSSpec.Env {
diff --git a/pkg/instrumentation/nodejs_test.go b/pkg/instrumentation/nodejs_test.go
index f5a8bf93ad..e0a187f0ab 100644
--- a/pkg/instrumentation/nodejs_test.go
+++ b/pkg/instrumentation/nodejs_test.go
@@ -174,7 +174,7 @@ func TestInjectNodeJSSDK(t *testing.T) {
 
 	for _, test := range tests {
 		t.Run(test.name, func(t *testing.T) {
-			pod := injectNodeJSSDK(logr.Discard(), test.NodeJS, test.pod)
+			pod := injectNodeJSSDK(logr.Discard(), test.NodeJS, test.pod, 0)
 			assert.Equal(t, test.expected, pod)
 		})
 	}
diff --git a/pkg/instrumentation/podmutator.go b/pkg/instrumentation/podmutator.go
index ba40d73b51..03e6267fc9 100644
--- a/pkg/instrumentation/podmutator.go
+++ b/pkg/instrumentation/podmutator.go
@@ -94,9 +94,12 @@ func (pm *instPodMutator) Mutate(ctx context.Context, ns corev1.Namespace, pod c
 		return pod, nil
 	}
 
+	// We retrieve the annotation for podname
+	var containerTarget = annotationValue(ns.ObjectMeta, pod.ObjectMeta, annotationInjectContainerName)
+
 	// once it's been determined that instrumentation is desired, none exists yet, and we know which instance it should talk to,
 	// we should inject the instrumentation.
-	return pm.sdkInjector.inject(ctx, insts, ns, pod), nil
+	return pm.sdkInjector.inject(ctx, insts, ns, pod, containerTarget), nil
 }
 
 func (pm *instPodMutator) getInstrumentationInstance(ctx context.Context, ns corev1.Namespace, pod corev1.Pod, instAnnotation string) (*v1alpha1.Instrumentation, error) {
diff --git a/pkg/instrumentation/python.go b/pkg/instrumentation/python.go
index d6ebdddb97..92bb0ddf49 100644
--- a/pkg/instrumentation/python.go
+++ b/pkg/instrumentation/python.go
@@ -30,9 +30,9 @@ const (
 	pythonPathSuffix      = "/otel-auto-instrumentation"
 )
 
-func injectPythonSDK(logger logr.Logger, pythonSpec v1alpha1.Python, pod corev1.Pod) corev1.Pod {
+func injectPythonSDK(logger logr.Logger, pythonSpec v1alpha1.Python, pod corev1.Pod, index int) corev1.Pod {
 	// caller checks if there is at least one container
-	container := &pod.Spec.Containers[0]
+	container := &pod.Spec.Containers[index]
 
 	// inject env vars
 	for _, env := range pythonSpec.Env {
diff --git a/pkg/instrumentation/python_test.go b/pkg/instrumentation/python_test.go
index 3fa6d68b2a..2d510fca38 100644
--- a/pkg/instrumentation/python_test.go
+++ b/pkg/instrumentation/python_test.go
@@ -244,7 +244,7 @@ func TestInjectPythonSDK(t *testing.T) {
 
 	for _, test := range tests {
 		t.Run(test.name, func(t *testing.T) {
-			pod := injectPythonSDK(logr.Discard(), test.Python, test.pod)
+			pod := injectPythonSDK(logr.Discard(), test.Python, test.pod, 0)
 			assert.Equal(t, test.expected, pod)
 		})
 	}
diff --git a/pkg/instrumentation/sdk.go b/pkg/instrumentation/sdk.go
index 161e08ad29..eb94fafe3f 100644
--- a/pkg/instrumentation/sdk.go
+++ b/pkg/instrumentation/sdk.go
@@ -56,39 +56,48 @@ type sdkInjector struct {
 	client client.Client
 }
 
-func (i *sdkInjector) inject(ctx context.Context, insts languageInstrumentations, ns corev1.Namespace, pod corev1.Pod) corev1.Pod {
+func (i *sdkInjector) inject(ctx context.Context, insts languageInstrumentations, ns corev1.Namespace, pod corev1.Pod, containerName string) corev1.Pod {
 	if len(pod.Spec.Containers) < 1 {
 		return pod
 	}
 
+	// We search for specific container to inject variables and if no one is found
+	// We fallback to first container
+	var index = 0
+	for idx, ctnair := range pod.Spec.Containers {
+		if ctnair.Name == containerName {
+			index = idx
+		}
+	}
+
 	// inject only to the first container for now
 	// in the future we can define an annotation to configure this
 	if insts.Java != nil {
 		otelinst := *insts.Java
 		i.logger.V(1).Info("injecting java instrumentation into pod", "otelinst-namespace", otelinst.Namespace, "otelinst-name", otelinst.Name)
-		pod = injectJavaagent(i.logger, otelinst.Spec.Java, pod)
-		pod = i.injectCommonEnvVar(otelinst, pod)
-		pod = i.injectCommonSDKConfig(ctx, otelinst, ns, pod)
+		pod = injectJavaagent(i.logger, otelinst.Spec.Java, pod, index)
+		pod = i.injectCommonEnvVar(otelinst, pod, index)
+		pod = i.injectCommonSDKConfig(ctx, otelinst, ns, pod, index)
 	}
 	if insts.NodeJS != nil {
 		otelinst := *insts.NodeJS
 		i.logger.V(1).Info("injecting nodejs instrumentation into pod", "otelinst-namespace", otelinst.Namespace, "otelinst-name", otelinst.Name)
-		pod = injectNodeJSSDK(i.logger, otelinst.Spec.NodeJS, pod)
-		pod = i.injectCommonEnvVar(otelinst, pod)
-		pod = i.injectCommonSDKConfig(ctx, otelinst, ns, pod)
+		pod = injectNodeJSSDK(i.logger, otelinst.Spec.NodeJS, pod, index)
+		pod = i.injectCommonEnvVar(otelinst, pod, index)
+		pod = i.injectCommonSDKConfig(ctx, otelinst, ns, pod, index)
 	}
 	if insts.Python != nil {
 		otelinst := *insts.Python
 		i.logger.V(1).Info("injecting python instrumentation into pod", "otelinst-namespace", otelinst.Namespace, "otelinst-name", otelinst.Name)
-		pod = injectPythonSDK(i.logger, otelinst.Spec.Python, pod)
-		pod = i.injectCommonEnvVar(otelinst, pod)
-		pod = i.injectCommonSDKConfig(ctx, otelinst, ns, pod)
+		pod = injectPythonSDK(i.logger, otelinst.Spec.Python, pod, index)
+		pod = i.injectCommonEnvVar(otelinst, pod, index)
+		pod = i.injectCommonSDKConfig(ctx, otelinst, ns, pod, index)
 	}
 	return pod
 }
 
-func (i *sdkInjector) injectCommonEnvVar(otelinst v1alpha1.Instrumentation, pod corev1.Pod) corev1.Pod {
-	container := &pod.Spec.Containers[0]
+func (i *sdkInjector) injectCommonEnvVar(otelinst v1alpha1.Instrumentation, pod corev1.Pod, index int) corev1.Pod {
+	container := &pod.Spec.Containers[index]
 	for _, env := range otelinst.Spec.Env {
 		idx := getIndexOfEnv(container.Env, env.Name)
 		if idx == -1 {
@@ -98,8 +107,8 @@ func (i *sdkInjector) injectCommonEnvVar(otelinst v1alpha1.Instrumentation, pod
 	return pod
 }
 
-func (i *sdkInjector) injectCommonSDKConfig(ctx context.Context, otelinst v1alpha1.Instrumentation, ns corev1.Namespace, pod corev1.Pod) corev1.Pod {
-	container := &pod.Spec.Containers[0]
+func (i *sdkInjector) injectCommonSDKConfig(ctx context.Context, otelinst v1alpha1.Instrumentation, ns corev1.Namespace, pod corev1.Pod, index int) corev1.Pod {
+	container := &pod.Spec.Containers[index]
 	resourceMap := i.createResourceMap(ctx, otelinst, ns, pod)
 	idx := getIndexOfEnv(container.Env, envOTELServiceName)
 	if idx == -1 {
diff --git a/pkg/instrumentation/sdk_test.go b/pkg/instrumentation/sdk_test.go
index 4ee0e63c0f..4b9659439f 100644
--- a/pkg/instrumentation/sdk_test.go
+++ b/pkg/instrumentation/sdk_test.go
@@ -364,7 +364,7 @@ func TestSDKInjection(t *testing.T) {
 			inj := sdkInjector{
 				client: k8sClient,
 			}
-			pod := inj.injectCommonSDKConfig(context.Background(), test.inst, corev1.Namespace{ObjectMeta: metav1.ObjectMeta{Name: test.pod.Namespace}}, test.pod)
+			pod := inj.injectCommonSDKConfig(context.Background(), test.inst, corev1.Namespace{ObjectMeta: metav1.ObjectMeta{Name: test.pod.Namespace}}, test.pod, 0)
 			_, err = json.MarshalIndent(pod, "", "  ")
 			assert.NoError(t, err)
 			assert.Equal(t, test.expected, pod)
@@ -399,7 +399,7 @@ func TestInjectJava(t *testing.T) {
 					},
 				},
 			},
-		})
+		}, "")
 	assert.Equal(t, corev1.Pod{
 		Spec: corev1.PodSpec{
 			Volumes: []corev1.Volume{
@@ -497,7 +497,7 @@ func TestInjectNodeJS(t *testing.T) {
 					},
 				},
 			},
-		})
+		}, "")
 	assert.Equal(t, corev1.Pod{
 		Spec: corev1.PodSpec{
 			Volumes: []corev1.Volume{
@@ -596,7 +596,7 @@ func TestInjectPython(t *testing.T) {
 					},
 				},
 			},
-		})
+		}, "")
 	assert.Equal(t, corev1.Pod{
 		Spec: corev1.PodSpec{
 			Volumes: []corev1.Volume{