diff --git a/staging/src/k8s.io/apiserver/pkg/admission/plugin/policy/mutating/patch/smd.go b/staging/src/k8s.io/apiserver/pkg/admission/plugin/policy/mutating/patch/smd.go
index 3be79df54ea..7135aca3a25 100644
--- a/staging/src/k8s.io/apiserver/pkg/admission/plugin/policy/mutating/patch/smd.go
+++ b/staging/src/k8s.io/apiserver/pkg/admission/plugin/policy/mutating/patch/smd.go
@@ -138,7 +138,7 @@ func ApplyStructuredMergeDiff(
 		return nil, fmt.Errorf("invalid ApplyConfiguration: %w", err)
 	}
 
-	liveObjTyped, err := typeConverter.ObjectToTyped(originalObject)
+	liveObjTyped, err := typeConverter.ObjectToTyped(originalObject, typed.AllowDuplicates)
 	if err != nil {
 		return nil, fmt.Errorf("failed to convert original object to typed object: %w", err)
 	}
diff --git a/staging/src/k8s.io/apiserver/pkg/admission/plugin/policy/mutating/patch/smd_test.go b/staging/src/k8s.io/apiserver/pkg/admission/plugin/policy/mutating/patch/smd_test.go
index e4e3810a0d6..3f0b87233dc 100644
--- a/staging/src/k8s.io/apiserver/pkg/admission/plugin/policy/mutating/patch/smd_test.go
+++ b/staging/src/k8s.io/apiserver/pkg/admission/plugin/policy/mutating/patch/smd_test.go
@@ -233,6 +233,107 @@ func TestApplyConfiguration(t *testing.T) {
 			object:      &appsv1.Deployment{Spec: appsv1.DeploymentSpec{Replicas: ptr.To[int32](1)}},
 			expectedErr: "must evaluate to Object but got Object.spec.metadata",
 		},
+		{
+			name: "apply configuration with duplicate env vars in original object",
+			expression: `Object{
+					spec: Object.spec{
+						replicas: 3
+					}
+				}`,
+			gvr: deploymentGVR,
+			object: &appsv1.Deployment{
+				Spec: appsv1.DeploymentSpec{
+					Replicas: ptr.To[int32](1),
+					Template: corev1.PodTemplateSpec{
+						Spec: corev1.PodSpec{
+							Containers: []corev1.Container{{
+								Name: "nginx",
+								Env: []corev1.EnvVar{
+									{Name: "test", Value: "a"},
+									{Name: "test", Value: "b"},
+								},
+							}},
+						},
+					},
+				},
+			},
+			expectedResult: &appsv1.Deployment{
+				Spec: appsv1.DeploymentSpec{
+					Replicas: ptr.To[int32](3),
+					Template: corev1.PodTemplateSpec{
+						Spec: corev1.PodSpec{
+							Containers: []corev1.Container{{
+								Name: "nginx",
+								Env: []corev1.EnvVar{
+									{Name: "test", Value: "a"},
+									{Name: "test", Value: "b"},
+								},
+							}},
+						},
+					},
+				},
+			},
+		},
+		// This test verifies that modifying an existing environment variable works correctly,
+		// even if the original object contains duplicates.
+		// Because 'env' is defined with `listType=map` and `listMapKey=name` in the schema,
+		// Structured Merge Diff (SMD) treats 'name' as the unique key.
+		// When the patch updates the entry with name="test", SMD merges the changes.
+		// As a side effect of the merge process on a map-type list, duplicate entries for the
+		// same key in the original object are consolidated into a single entry in the result.
+		// This matches the behavior of Server-Side Apply (SSA) and kubectl apply.
+		{
+			name: "apply configuration modify existing env variable",
+			expression: `Object{
+					spec: Object.spec{
+						template: Object.spec.template{
+							spec: Object.spec.template.spec{
+								containers: [Object.spec.template.spec.containers{
+									name: "nginx",
+									env: [Object.spec.template.spec.containers.env{
+										name: "test",
+										value: "c"
+									}]
+								}]
+							}
+						}
+					}
+				}`,
+			gvr: deploymentGVR,
+			object: &appsv1.Deployment{
+				Spec: appsv1.DeploymentSpec{
+					Replicas: ptr.To[int32](1),
+					Template: corev1.PodTemplateSpec{
+						Spec: corev1.PodSpec{
+							Containers: []corev1.Container{{
+								Name: "nginx",
+								Env: []corev1.EnvVar{
+									{Name: "test", Value: "a"},
+									{Name: "test", Value: "b"},
+									{Name: "foo", Value: "bar"},
+								},
+							}},
+						},
+					},
+				},
+			},
+			expectedResult: &appsv1.Deployment{
+				Spec: appsv1.DeploymentSpec{
+					Replicas: ptr.To[int32](1),
+					Template: corev1.PodTemplateSpec{
+						Spec: corev1.PodSpec{
+							Containers: []corev1.Container{{
+								Name: "nginx",
+								Env: []corev1.EnvVar{
+									{Name: "test", Value: "c"},
+									{Name: "foo", Value: "bar"},
+								},
+							}},
+						},
+					},
+				},
+			},
+		},
 	}
 
 	compiler, err := cel.NewCompositedCompiler(environment.MustBaseEnvSet(environment.DefaultCompatibilityVersion()))