diff --git a/apis/v1alpha1/instrumentation_types.go b/apis/v1alpha1/instrumentation_types.go
index 37e2592546..e682146e21 100644
--- a/apis/v1alpha1/instrumentation_types.go
+++ b/apis/v1alpha1/instrumentation_types.go
@@ -37,7 +37,9 @@ type InstrumentationSpec struct {
 	// +optional
 	Sampler `json:"sampler,omitempty"`
 
-	// Env defines env vars.
+	// Env defines common env vars. There are four layers for env vars' definitions and
+	// 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.
 	// +optional
 	Env []corev1.EnvVar `json:"env,omitempty"`
 
@@ -94,7 +96,9 @@ type Java struct {
 	// +optional
 	Image string `json:"image,omitempty"`
 
-	// Env defines env vars.
+	// Env defines java specific env vars. There are four layers for env vars' definitions and
+	// 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.
 	// +optional
 	Env []corev1.EnvVar `json:"env,omitempty"`
 }
@@ -105,7 +109,9 @@ type NodeJS struct {
 	// +optional
 	Image string `json:"image,omitempty"`
 
-	// Env defines env vars.
+	// Env defines nodejs specific env vars. There are four layers for env vars' definitions and
+	// 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.
 	// +optional
 	Env []corev1.EnvVar `json:"env,omitempty"`
 }
@@ -116,7 +122,9 @@ type Python struct {
 	// +optional
 	Image string `json:"image,omitempty"`
 
-	// Env defines env vars.
+	// Env defines python specific env vars. There are four layers for env vars' definitions and
+	// 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.
 	// +optional
 	Env []corev1.EnvVar `json:"env,omitempty"`
 }
diff --git a/apis/v1alpha1/instrumentation_webhook.go b/apis/v1alpha1/instrumentation_webhook.go
index 800e8d1781..1a977ee192 100644
--- a/apis/v1alpha1/instrumentation_webhook.go
+++ b/apis/v1alpha1/instrumentation_webhook.go
@@ -16,10 +16,10 @@ package v1alpha1
 
 import (
 	"fmt"
-	corev1 "k8s.io/api/core/v1"
 	"strconv"
 	"strings"
 
+	corev1 "k8s.io/api/core/v1"
 	"k8s.io/apimachinery/pkg/runtime"
 	ctrl "sigs.k8s.io/controller-runtime"
 	logf "sigs.k8s.io/controller-runtime/pkg/log"
@@ -129,11 +129,9 @@ func (in *Instrumentation) validate() error {
 }
 
 func (in *Instrumentation) validateEnv(envs []corev1.EnvVar) error {
-	if len(envs) > 0 {
-		for _, env := range envs {
-			if !strings.HasPrefix(env.Name, envPrefix) {
-				return fmt.Errorf("env name should start with \"OTEL_\": %s", env.Name)
-			}
+	for _, env := range envs {
+		if !strings.HasPrefix(env.Name, envPrefix) {
+			return fmt.Errorf("env name should start with \"OTEL_\": %s", env.Name)
 		}
 	}
 	return nil
diff --git a/config/crd/bases/opentelemetry.io_instrumentations.yaml b/config/crd/bases/opentelemetry.io_instrumentations.yaml
index 2a5789397e..0fcc3cc159 100644
--- a/config/crd/bases/opentelemetry.io_instrumentations.yaml
+++ b/config/crd/bases/opentelemetry.io_instrumentations.yaml
@@ -45,7 +45,11 @@ 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 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.
@@ -160,7 +164,11 @@ 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 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.
@@ -278,7 +286,11 @@ 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 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.
@@ -411,7 +423,11 @@ 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 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/docs/api.md b/docs/api.md
index 9d35c0bce8..86ad531765 100644
--- a/docs/api.md
+++ b/docs/api.md
@@ -89,7 +89,7 @@ InstrumentationSpec defines the desired state of OpenTelemetry SDK and instrumen
         <td><b><a href="#instrumentationspecenvindex">env</a></b></td>
         <td>[]object</td>
         <td>
-          Env defines env vars.<br/>
+          Env defines common env vars. There are four layers for env vars' definitions and 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.<br/>
         </td>
         <td>false</td>
       </tr><tr>
@@ -438,7 +438,7 @@ Java defines configuration for java auto-instrumentation.
         <td><b><a href="#instrumentationspecjavaenvindex">env</a></b></td>
         <td>[]object</td>
         <td>
-          Env defines env vars.<br/>
+          Env defines java specific env vars. There are four layers for env vars' definitions and 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.<br/>
         </td>
         <td>false</td>
       </tr><tr>
@@ -718,7 +718,7 @@ NodeJS defines configuration for nodejs auto-instrumentation.
         <td><b><a href="#instrumentationspecnodejsenvindex">env</a></b></td>
         <td>[]object</td>
         <td>
-          Env defines env vars.<br/>
+          Env defines nodejs specific env vars. There are four layers for env vars' definitions and 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.<br/>
         </td>
         <td>false</td>
       </tr><tr>
@@ -998,7 +998,7 @@ Python defines configuration for python auto-instrumentation.
         <td><b><a href="#instrumentationspecpythonenvindex">env</a></b></td>
         <td>[]object</td>
         <td>
-          Env defines env vars.<br/>
+          Env defines python specific env vars. There are four layers for env vars' definitions and 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.<br/>
         </td>
         <td>false</td>
       </tr><tr>
diff --git a/tests/e2e/instrumentation-java/00-install-instrumentation.yaml b/tests/e2e/instrumentation-java/00-install-instrumentation.yaml
index 6c1347b139..793f5a87f7 100644
--- a/tests/e2e/instrumentation-java/00-install-instrumentation.yaml
+++ b/tests/e2e/instrumentation-java/00-install-instrumentation.yaml
@@ -3,6 +3,17 @@ kind: Instrumentation
 metadata:
   name: java
 spec:
+  env:
+    - 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:
     endpoint: http://localhost:4317
   propagators:
@@ -11,3 +22,9 @@ spec:
   sampler:
     type: parentbased_traceidratio
     argument: "0.25"
+  java:
+    env:
+    - name: OTEL_JAVAAGENT_DEBUG
+      value: "true"
+    - name: OTEL_INSTRUMENTATION_JDBC_ENABLED
+      value: "false"
diff --git a/tests/e2e/instrumentation-java/01-assert.yaml b/tests/e2e/instrumentation-java/01-assert.yaml
index 63b4bd8330..cdc33dcc36 100644
--- a/tests/e2e/instrumentation-java/01-assert.yaml
+++ b/tests/e2e/instrumentation-java/01-assert.yaml
@@ -10,21 +10,29 @@ spec:
   containers:
   - name: myapp
     env:
-    - name: OTEL_SERVICE_NAME
-      value: my-deployment-with-sidecar
+    - name: OTEL_JAVAAGENT_DEBUG
+      value: "true"
+    - name: OTEL_INSTRUMENTATION_JDBC_ENABLED
+      value: "false"
+    - name: JAVA_TOOL_OPTIONS
+      value: " -javaagent:/otel-auto-instrumentation/javaagent.jar"
+    - 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"
+    - name: OTEL_SERVICE_NAME
+      value: my-deployment-with-sidecar
     - name: OTEL_RESOURCE_ATTRIBUTES_POD_NAME
     - name: OTEL_RESOURCE_ATTRIBUTES_NODE_NAME
     - name: OTEL_RESOURCE_ATTRIBUTES
     - name: OTEL_PROPAGATORS
       value: jaeger,b3
-    - name: OTEL_TRACES_SAMPLER
-      value: parentbased_traceidratio
-    - name: OTEL_TRACES_SAMPLER_ARG
-      value: "0.25"
-    - name: JAVA_TOOL_OPTIONS
-      value: " -javaagent:/otel-auto-instrumentation/javaagent.jar"
     volumeMounts:
     - mountPath: /var/run/secrets/kubernetes.io/serviceaccount
     - mountPath: /otel-auto-instrumentation
diff --git a/tests/e2e/instrumentation-nodejs/00-install-instrumentation.yaml b/tests/e2e/instrumentation-nodejs/00-install-instrumentation.yaml
index 9ea4358b9b..40459f483a 100644
--- a/tests/e2e/instrumentation-nodejs/00-install-instrumentation.yaml
+++ b/tests/e2e/instrumentation-nodejs/00-install-instrumentation.yaml
@@ -3,8 +3,27 @@ kind: Instrumentation
 metadata:
   name: nodejs
 spec:
+  env:
+    - 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:
     endpoint: http://localhost:4317
   propagators:
     - jaeger
     - b3
+  sampler:
+    type: parentbased_traceidratio
+    argument: "0.25"
+  nodejs:
+    env:
+      - name: OTEL_NODEJS_DEBUG
+        value: "true"
+
diff --git a/tests/e2e/instrumentation-nodejs/01-assert.yaml b/tests/e2e/instrumentation-nodejs/01-assert.yaml
index b796a5b8e5..d327e85962 100644
--- a/tests/e2e/instrumentation-nodejs/01-assert.yaml
+++ b/tests/e2e/instrumentation-nodejs/01-assert.yaml
@@ -10,17 +10,27 @@ spec:
   containers:
   - name: myapp
     env:
-    - name: OTEL_SERVICE_NAME
-      value: my-deployment-with-sidecar
+    - name: OTEL_NODEJS_DEBUG
+      value: "true"
+    - name: NODE_OPTIONS
+      value: " --require /otel-auto-instrumentation/autoinstrumentation.js"
+    - 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"
+    - name: OTEL_SERVICE_NAME
+      value: my-deployment-with-sidecar
     - name: OTEL_RESOURCE_ATTRIBUTES_POD_NAME
     - name: OTEL_RESOURCE_ATTRIBUTES_NODE_NAME
     - name: OTEL_RESOURCE_ATTRIBUTES
     - name: OTEL_PROPAGATORS
       value: jaeger,b3
-    - name: NODE_OPTIONS
-      value: " --require /otel-auto-instrumentation/autoinstrumentation.js"
     volumeMounts:
     - mountPath: /var/run/secrets/kubernetes.io/serviceaccount
     - mountPath: /otel-auto-instrumentation
diff --git a/tests/e2e/instrumentation-python/00-install-instrumentation.yaml b/tests/e2e/instrumentation-python/00-install-instrumentation.yaml
index d41827bf8f..fa1fff2353 100644
--- a/tests/e2e/instrumentation-python/00-install-instrumentation.yaml
+++ b/tests/e2e/instrumentation-python/00-install-instrumentation.yaml
@@ -3,8 +3,26 @@ kind: Instrumentation
 metadata:
   name: python
 spec:
+  env:
+    - name: OTEL_EXPORTER_OTLP_TIMEOUT
+      value: "20"
+    - name: OTEL_TRACES_SAMPLER
+      value: parentbased_traceidratio
+    - name: OTEL_TRACES_SAMPLER_ARG
+      value: "0.85"
   exporter:
-    endpoint: http://localhost:4318/v1/traces
+    endpoint: http://localhost:4317
   propagators:
     - jaeger
     - b3
+  sampler:
+    type: parentbased_traceidratio
+    argument: "0.25"
+  python:
+    env:
+      - name: OTEL_LOG_LEVEL
+        value: "debug"
+      - name: OTEL_TRACES_EXPORTER
+        value: otlp_proto_http
+      - name: OTEL_EXPORTER_OTLP_ENDPOINT
+        value: http://localhost:4317
\ No newline at end of file
diff --git a/tests/e2e/instrumentation-python/01-assert.yaml b/tests/e2e/instrumentation-python/01-assert.yaml
index 35ea2acb80..105cfd30cd 100644
--- a/tests/e2e/instrumentation-python/01-assert.yaml
+++ b/tests/e2e/instrumentation-python/01-assert.yaml
@@ -10,19 +10,27 @@ spec:
   containers:
   - name: myapp
     env:
+    - name: OTEL_LOG_LEVEL
+      value: "debug"
+    - name: OTEL_TRACES_EXPORTER
+      value: otlp_proto_http
+    - name: OTEL_EXPORTER_OTLP_ENDPOINT
+      value: http://localhost:4317
+    - name: PYTHONPATH
+      value: "/otel-auto-instrumentation/opentelemetry/instrumentation/auto_instrumentation:/otel-auto-instrumentation"
+    - 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: my-deployment-with-sidecar
-    - name: OTEL_EXPORTER_OTLP_ENDPOINT
-      value: http://localhost:4318/v1/traces
     - name: OTEL_RESOURCE_ATTRIBUTES_POD_NAME
     - name: OTEL_RESOURCE_ATTRIBUTES_NODE_NAME
     - name: OTEL_RESOURCE_ATTRIBUTES
     - name: OTEL_PROPAGATORS
       value: jaeger,b3
-    - name: PYTHONPATH
-      value: "/otel-auto-instrumentation/opentelemetry/instrumentation/auto_instrumentation:/otel-auto-instrumentation"
-    - name: OTEL_TRACES_EXPORTER
-      value: otlp_proto_http
     volumeMounts:
     - mountPath: /var/run/secrets/kubernetes.io/serviceaccount
     - mountPath: /otel-auto-instrumentation