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/bundle/manifests/opentelemetry.io_instrumentations.yaml b/bundle/manifests/opentelemetry.io_instrumentations.yaml
index 7b513cae68..13321f7c89 100644
--- a/bundle/manifests/opentelemetry.io_instrumentations.yaml
+++ b/bundle/manifests/opentelemetry.io_instrumentations.yaml
@@ -43,7 +43,11 @@ spec:
               SDK and instrumentation.
             properties:
               env:
-                description: Env defines env vars.
+                description: 'Env defines common env vars. There are four layers for
+                  env vars'' definitions and the precedence order is: `original container
+                  env vars` > `language specific env vars` > `common env vars` > `instrument
+                  spec configs'' vars`. If the former var had been defined, then the
+                  other vars would be ignored.'
                 items:
                   description: EnvVar represents an environment variable present in
                     a Container.
@@ -158,7 +162,11 @@ spec:
                 description: Java defines configuration for java auto-instrumentation.
                 properties:
                   env:
-                    description: Env defines env vars.
+                    description: 'Env defines java specific env vars. There are four
+                      layers for env vars'' definitions and the precedence order is:
+                      `original container env vars` > `language specific env vars`
+                      > `common env vars` > `instrument spec configs'' vars`. If the
+                      former var had been defined, then the other vars would be ignored.'
                     items:
                       description: EnvVar represents an environment variable present
                         in a Container.
@@ -276,7 +284,11 @@ spec:
                 description: NodeJS defines configuration for nodejs auto-instrumentation.
                 properties:
                   env:
-                    description: Env defines env vars.
+                    description: 'Env defines nodejs specific env vars. There are
+                      four layers for env vars'' definitions and the precedence order
+                      is: `original container env vars` > `language specific env vars`
+                      > `common env vars` > `instrument spec configs'' vars`. If the
+                      former var had been defined, then the other vars would be ignored.'
                     items:
                       description: EnvVar represents an environment variable present
                         in a Container.
@@ -409,7 +421,11 @@ spec:
                 description: Python defines configuration for python auto-instrumentation.
                 properties:
                   env:
-                    description: Env defines env vars.
+                    description: 'Env defines python specific env vars. There are
+                      four layers for env vars'' definitions and the precedence order
+                      is: `original container env vars` > `language specific env vars`
+                      > `common env vars` > `instrument spec configs'' vars`. If the
+                      former var had been defined, then the other vars would be ignored.'
                     items:
                       description: EnvVar represents an environment variable present
                         in a Container.
diff --git a/pkg/instrumentation/podmutator_test.go b/pkg/instrumentation/podmutator_test.go
index 2512fd832d..15766b7a44 100644
--- a/pkg/instrumentation/podmutator_test.go
+++ b/pkg/instrumentation/podmutator_test.go
@@ -53,7 +53,40 @@ func TestMutatePod(t *testing.T) {
 					Namespace: "javaagent",
 				},
 				Spec: v1alpha1.InstrumentationSpec{
-					Java: v1alpha1.Java{},
+					Java: v1alpha1.Java{
+						Env: []corev1.EnvVar{
+							{
+								Name:  "OTEL_JAVAAGENT_DEBUG",
+								Value: "true",
+							},
+							{
+								Name:  "OTEL_INSTRUMENTATION_JDBC_ENABLED",
+								Value: "false",
+							},
+						},
+					},
+					Env: []corev1.EnvVar{
+						{
+							Name:  "OTEL_TRACES_EXPORTER",
+							Value: "otlp",
+						},
+						{
+							Name:  "OTEL_EXPORTER_OTLP_ENDPOINT",
+							Value: "http://localhost:4317",
+						},
+						{
+							Name:  "OTEL_EXPORTER_OTLP_TIMEOUT",
+							Value: "20",
+						},
+						{
+							Name:  "OTEL_TRACES_SAMPLER",
+							Value: "parentbased_traceidratio",
+						},
+						{
+							Name:  "OTEL_TRACES_SAMPLER_ARG",
+							Value: "0.85",
+						},
+					},
 					Exporter: v1alpha1.Exporter{
 						Endpoint: "http://collector:12345",
 					},
@@ -103,12 +136,40 @@ func TestMutatePod(t *testing.T) {
 							Name: "app",
 							Env: []corev1.EnvVar{
 								{
-									Name:  "OTEL_SERVICE_NAME",
-									Value: "app",
+									Name:  "OTEL_JAVAAGENT_DEBUG",
+									Value: "true",
+								},
+								{
+									Name:  "OTEL_INSTRUMENTATION_JDBC_ENABLED",
+									Value: "false",
+								},
+								{
+									Name:  "JAVA_TOOL_OPTIONS",
+									Value: javaJVMArgument,
+								},
+								{
+									Name:  "OTEL_TRACES_EXPORTER",
+									Value: "otlp",
 								},
 								{
 									Name:  "OTEL_EXPORTER_OTLP_ENDPOINT",
-									Value: "http://collector:12345",
+									Value: "http://localhost:4317",
+								},
+								{
+									Name:  "OTEL_EXPORTER_OTLP_TIMEOUT",
+									Value: "20",
+								},
+								{
+									Name:  "OTEL_TRACES_SAMPLER",
+									Value: "parentbased_traceidratio",
+								},
+								{
+									Name:  "OTEL_TRACES_SAMPLER_ARG",
+									Value: "0.85",
+								},
+								{
+									Name:  "OTEL_SERVICE_NAME",
+									Value: "app",
 								},
 								{
 									Name: "OTEL_RESOURCE_ATTRIBUTES_POD_NAME",
@@ -130,10 +191,6 @@ func TestMutatePod(t *testing.T) {
 									Name:  "OTEL_RESOURCE_ATTRIBUTES",
 									Value: "k8s.container.name=app,k8s.namespace.name=javaagent,k8s.node.name=$(OTEL_RESOURCE_ATTRIBUTES_NODE_NAME),k8s.pod.name=$(OTEL_RESOURCE_ATTRIBUTES_POD_NAME)",
 								},
-								{
-									Name:  "JAVA_TOOL_OPTIONS",
-									Value: javaJVMArgument,
-								},
 							},
 							VolumeMounts: []corev1.VolumeMount{
 								{
@@ -161,6 +218,34 @@ func TestMutatePod(t *testing.T) {
 				Spec: v1alpha1.InstrumentationSpec{
 					NodeJS: v1alpha1.NodeJS{
 						Image: "otel/nodejs:1",
+						Env: []corev1.EnvVar{
+							{
+								Name:  "OTEL_NODEJS_DEBUG",
+								Value: "true",
+							},
+						},
+					},
+					Env: []corev1.EnvVar{
+						{
+							Name:  "OTEL_TRACES_EXPORTER",
+							Value: "otlp",
+						},
+						{
+							Name:  "OTEL_EXPORTER_OTLP_ENDPOINT",
+							Value: "http://localhost:4317",
+						},
+						{
+							Name:  "OTEL_EXPORTER_OTLP_TIMEOUT",
+							Value: "20",
+						},
+						{
+							Name:  "OTEL_TRACES_SAMPLER",
+							Value: "parentbased_traceidratio",
+						},
+						{
+							Name:  "OTEL_TRACES_SAMPLER_ARG",
+							Value: "0.85",
+						},
 					},
 					Exporter: v1alpha1.Exporter{
 						Endpoint: "http://collector:12345",
@@ -212,12 +297,36 @@ func TestMutatePod(t *testing.T) {
 							Name: "app",
 							Env: []corev1.EnvVar{
 								{
-									Name:  "OTEL_SERVICE_NAME",
-									Value: "app",
+									Name:  "OTEL_NODEJS_DEBUG",
+									Value: "true",
+								},
+								{
+									Name:  "NODE_OPTIONS",
+									Value: nodeRequireArgument,
+								},
+								{
+									Name:  "OTEL_TRACES_EXPORTER",
+									Value: "otlp",
 								},
 								{
 									Name:  "OTEL_EXPORTER_OTLP_ENDPOINT",
-									Value: "http://collector:12345",
+									Value: "http://localhost:4317",
+								},
+								{
+									Name:  "OTEL_EXPORTER_OTLP_TIMEOUT",
+									Value: "20",
+								},
+								{
+									Name:  "OTEL_TRACES_SAMPLER",
+									Value: "parentbased_traceidratio",
+								},
+								{
+									Name:  "OTEL_TRACES_SAMPLER_ARG",
+									Value: "0.85",
+								},
+								{
+									Name:  "OTEL_SERVICE_NAME",
+									Value: "app",
 								},
 								{
 									Name: "OTEL_RESOURCE_ATTRIBUTES_POD_NAME",
@@ -239,10 +348,6 @@ func TestMutatePod(t *testing.T) {
 									Name:  "OTEL_RESOURCE_ATTRIBUTES",
 									Value: "k8s.container.name=app,k8s.namespace.name=nodejs,k8s.node.name=$(OTEL_RESOURCE_ATTRIBUTES_NODE_NAME),k8s.pod.name=$(OTEL_RESOURCE_ATTRIBUTES_POD_NAME)",
 								},
-								{
-									Name:  "NODE_OPTIONS",
-									Value: nodeRequireArgument,
-								},
 							},
 							VolumeMounts: []corev1.VolumeMount{
 								{
@@ -270,10 +375,38 @@ func TestMutatePod(t *testing.T) {
 				Spec: v1alpha1.InstrumentationSpec{
 					Python: v1alpha1.Python{
 						Image: "otel/python:1",
+						Env: []corev1.EnvVar{
+							{
+								Name:  "OTEL_LOG_LEVEL",
+								Value: "debug",
+							},
+							{
+								Name:  "OTEL_TRACES_EXPORTER",
+								Value: "otlp_proto_http",
+							},
+							{
+								Name:  "OTEL_EXPORTER_OTLP_ENDPOINT",
+								Value: "http://localhost:4317",
+							},
+						},
 					},
 					Exporter: v1alpha1.Exporter{
 						Endpoint: "http://collector:12345",
 					},
+					Env: []corev1.EnvVar{
+						{
+							Name:  "OTEL_EXPORTER_OTLP_TIMEOUT",
+							Value: "20",
+						},
+						{
+							Name:  "OTEL_TRACES_SAMPLER",
+							Value: "parentbased_traceidratio",
+						},
+						{
+							Name:  "OTEL_TRACES_SAMPLER_ARG",
+							Value: "0.85",
+						},
+					},
 				},
 			},
 			pod: corev1.Pod{
@@ -321,12 +454,36 @@ func TestMutatePod(t *testing.T) {
 							Name: "app",
 							Env: []corev1.EnvVar{
 								{
-									Name:  "OTEL_SERVICE_NAME",
-									Value: "app",
+									Name:  "OTEL_LOG_LEVEL",
+									Value: "debug",
+								},
+								{
+									Name:  "OTEL_TRACES_EXPORTER",
+									Value: "otlp_proto_http",
 								},
 								{
 									Name:  "OTEL_EXPORTER_OTLP_ENDPOINT",
-									Value: "http://collector:12345",
+									Value: "http://localhost:4317",
+								},
+								{
+									Name:  "PYTHONPATH",
+									Value: fmt.Sprintf("%s:%s", pythonPathPrefix, pythonPathSuffix),
+								},
+								{
+									Name:  "OTEL_EXPORTER_OTLP_TIMEOUT",
+									Value: "20",
+								},
+								{
+									Name:  "OTEL_TRACES_SAMPLER",
+									Value: "parentbased_traceidratio",
+								},
+								{
+									Name:  "OTEL_TRACES_SAMPLER_ARG",
+									Value: "0.85",
+								},
+								{
+									Name:  "OTEL_SERVICE_NAME",
+									Value: "app",
 								},
 								{
 									Name: "OTEL_RESOURCE_ATTRIBUTES_POD_NAME",
@@ -348,14 +505,6 @@ func TestMutatePod(t *testing.T) {
 									Name:  "OTEL_RESOURCE_ATTRIBUTES",
 									Value: "k8s.container.name=app,k8s.namespace.name=python,k8s.node.name=$(OTEL_RESOURCE_ATTRIBUTES_NODE_NAME),k8s.pod.name=$(OTEL_RESOURCE_ATTRIBUTES_POD_NAME)",
 								},
-								{
-									Name:  "PYTHONPATH",
-									Value: fmt.Sprintf("%s:%s", pythonPathPrefix, pythonPathSuffix),
-								},
-								{
-									Name:  "OTEL_TRACES_EXPORTER",
-									Value: "otlp_proto_http",
-								},
 							},
 							VolumeMounts: []corev1.VolumeMount{
 								{
diff --git a/pkg/instrumentation/sdk_test.go b/pkg/instrumentation/sdk_test.go
index c667e73619..4ee0e63c0f 100644
--- a/pkg/instrumentation/sdk_test.go
+++ b/pkg/instrumentation/sdk_test.go
@@ -431,6 +431,10 @@ func TestInjectJava(t *testing.T) {
 						},
 					},
 					Env: []corev1.EnvVar{
+						{
+							Name:  "JAVA_TOOL_OPTIONS",
+							Value: javaJVMArgument,
+						},
 						{
 							Name:  "OTEL_SERVICE_NAME",
 							Value: "app",
@@ -459,10 +463,6 @@ func TestInjectJava(t *testing.T) {
 							Name:  "OTEL_RESOURCE_ATTRIBUTES",
 							Value: "k8s.container.name=app,k8s.node.name=$(OTEL_RESOURCE_ATTRIBUTES_NODE_NAME),k8s.pod.name=$(OTEL_RESOURCE_ATTRIBUTES_POD_NAME)",
 						},
-						{
-							Name:  "JAVA_TOOL_OPTIONS",
-							Value: javaJVMArgument,
-						},
 					},
 				},
 			},
@@ -529,6 +529,10 @@ func TestInjectNodeJS(t *testing.T) {
 						},
 					},
 					Env: []corev1.EnvVar{
+						{
+							Name:  "NODE_OPTIONS",
+							Value: nodeRequireArgument,
+						},
 						{
 							Name:  "OTEL_SERVICE_NAME",
 							Value: "app",
@@ -557,10 +561,6 @@ func TestInjectNodeJS(t *testing.T) {
 							Name:  "OTEL_RESOURCE_ATTRIBUTES",
 							Value: "k8s.container.name=app,k8s.node.name=$(OTEL_RESOURCE_ATTRIBUTES_NODE_NAME),k8s.pod.name=$(OTEL_RESOURCE_ATTRIBUTES_POD_NAME)",
 						},
-						{
-							Name:  "NODE_OPTIONS",
-							Value: nodeRequireArgument,
-						},
 					},
 				},
 			},
@@ -628,6 +628,14 @@ func TestInjectPython(t *testing.T) {
 						},
 					},
 					Env: []corev1.EnvVar{
+						{
+							Name:  "PYTHONPATH",
+							Value: fmt.Sprintf("%s:%s", pythonPathPrefix, pythonPathSuffix),
+						},
+						{
+							Name:  "OTEL_TRACES_EXPORTER",
+							Value: "otlp_proto_http",
+						},
 						{
 							Name:  "OTEL_SERVICE_NAME",
 							Value: "app",
@@ -656,14 +664,6 @@ func TestInjectPython(t *testing.T) {
 							Name:  "OTEL_RESOURCE_ATTRIBUTES",
 							Value: "k8s.container.name=app,k8s.node.name=$(OTEL_RESOURCE_ATTRIBUTES_NODE_NAME),k8s.pod.name=$(OTEL_RESOURCE_ATTRIBUTES_POD_NAME)",
 						},
-						{
-							Name:  "PYTHONPATH",
-							Value: fmt.Sprintf("%s:%s", pythonPathPrefix, pythonPathSuffix),
-						},
-						{
-							Name:  "OTEL_TRACES_EXPORTER",
-							Value: "otlp_proto_http",
-						},
 					},
 				},
 			},