diff --git a/pkg/instrumentation/annotationmutator.go b/pkg/instrumentation/annotationmutator.go
index 134916072..a6a46a779 100644
--- a/pkg/instrumentation/annotationmutator.go
+++ b/pkg/instrumentation/annotationmutator.go
@@ -35,7 +35,7 @@ func NewInsertAnnotationMutation(annotations map[string]string) AnnotationMutati
 }
 
 type removeAnnotationMutation struct {
-	remove []string
+	remove map[string]string
 }
 
 func (m *removeAnnotationMutation) Mutate(annotations map[string]string) map[string]string {
@@ -43,7 +43,7 @@ func (m *removeAnnotationMutation) Mutate(annotations map[string]string) map[str
 	if !m.shouldMutate(annotations) {
 		return mutatedAnnotations
 	}
-	for _, key := range m.remove {
+	for key := range m.remove {
 		if value, ok := annotations[key]; ok {
 			delete(annotations, key)
 			mutatedAnnotations[key] = value
@@ -52,18 +52,22 @@ func (m *removeAnnotationMutation) Mutate(annotations map[string]string) map[str
 	return mutatedAnnotations
 }
 
+// shouldMutate reports whether every managed key is present AND still carries the value the operator
+// injected. A key present with a different value (e.g. an explicit "false" opt-out set by the user) means
+// the annotation is not operator-owned, so the mutation must not remove it.
 func (m *removeAnnotationMutation) shouldMutate(annotations map[string]string) bool {
-	for _, key := range m.remove {
-		if _, ok := annotations[key]; !ok {
+	for key, managedValue := range m.remove {
+		if value, ok := annotations[key]; !ok || value != managedValue {
 			return false
 		}
 	}
 	return true
 }
 
-// NewRemoveAnnotationMutation creates a new mutation that removes annotations. All provided annotation keys
-// must be present for it to attempt to remove them.
-func NewRemoveAnnotationMutation(annotations []string) AnnotationMutation {
+// NewRemoveAnnotationMutation creates a new mutation that removes annotations. It only removes the provided
+// keys when all of them are present and each still carries the value it maps to (the value the operator
+// injected), so user-authored values are never destroyed.
+func NewRemoveAnnotationMutation(annotations map[string]string) AnnotationMutation {
 	return &removeAnnotationMutation{remove: annotations}
 }
 
diff --git a/pkg/instrumentation/annotationmutator_test.go b/pkg/instrumentation/annotationmutator_test.go
index 480b69b23..e3fb020d8 100644
--- a/pkg/instrumentation/annotationmutator_test.go
+++ b/pkg/instrumentation/annotationmutator_test.go
@@ -79,9 +79,9 @@ func TestMutateAnnotations(t *testing.T) {
 				"keyB": "2",
 			},
 			mutations: []AnnotationMutation{
-				NewRemoveAnnotationMutation([]string{
-					"keyA",
-					"keyC",
+				NewRemoveAnnotationMutation(map[string]string{
+					"keyA": "1",
+					"keyC": "4",
 				}),
 			},
 			wantAnnotations: map[string]string{
@@ -96,9 +96,9 @@ func TestMutateAnnotations(t *testing.T) {
 				"keyB": "2",
 			},
 			mutations: []AnnotationMutation{
-				NewRemoveAnnotationMutation([]string{
-					"keyA",
-					"keyB",
+				NewRemoveAnnotationMutation(map[string]string{
+					"keyA": "1",
+					"keyB": "2",
 				}),
 			},
 			wantAnnotations: map[string]string{},
@@ -113,11 +113,11 @@ func TestMutateAnnotations(t *testing.T) {
 				"keyB": "2",
 			},
 			mutations: []AnnotationMutation{
-				NewRemoveAnnotationMutation([]string{
-					"keyA",
+				NewRemoveAnnotationMutation(map[string]string{
+					"keyA": "1",
 				}),
-				NewRemoveAnnotationMutation([]string{
-					"keyB",
+				NewRemoveAnnotationMutation(map[string]string{
+					"keyB": "2",
 				}),
 			},
 			wantAnnotations: map[string]string{},
@@ -126,14 +126,33 @@ func TestMutateAnnotations(t *testing.T) {
 				"keyB": "2",
 			},
 		},
+		"TestRemove/PreservesUserValue": {
+			// A managed key present with a value other than the one the operator injected
+			// (e.g. an explicit "false" opt-out) must not be removed.
+			annotations: map[string]string{
+				"keyA": "false",
+				"keyB": "2",
+			},
+			mutations: []AnnotationMutation{
+				NewRemoveAnnotationMutation(map[string]string{
+					"keyA": "true",
+					"keyB": "2",
+				}),
+			},
+			wantAnnotations: map[string]string{
+				"keyA": "false",
+				"keyB": "2",
+			},
+			wantMutatedAnnotations: map[string]string{},
+		},
 		"TestBoth": {
 			annotations: map[string]string{
 				"keyA": "1",
 				"keyB": "2",
 			},
 			mutations: []AnnotationMutation{
-				NewRemoveAnnotationMutation([]string{
-					"keyA",
+				NewRemoveAnnotationMutation(map[string]string{
+					"keyA": "1",
 				}),
 				NewInsertAnnotationMutation(map[string]string{
 					"keyA": "3",
diff --git a/pkg/instrumentation/auto/annotation.go b/pkg/instrumentation/auto/annotation.go
index 90ed4d310..99f8dce3a 100644
--- a/pkg/instrumentation/auto/annotation.go
+++ b/pkg/instrumentation/auto/annotation.go
@@ -231,7 +231,7 @@ func newMutatorBuilder(typeSet instrumentation.TypeSet) *mutatorBuilder {
 func buildMutations(instType instrumentation.Type) (instrumentation.AnnotationMutation, instrumentation.AnnotationMutation) {
 	annotations := buildAnnotations(instType)
 	return instrumentation.NewInsertAnnotationMutation(annotations),
-		instrumentation.NewRemoveAnnotationMutation(maps.Keys(annotations))
+		instrumentation.NewRemoveAnnotationMutation(annotations)
 }
 
 // buildAnnotations creates an annotation map of the inject and auto-annotate keys.