diff --git a/v1/compile/compile.go b/v1/compile/compile.go
index e51c1f091f..7779f2435a 100644
--- a/v1/compile/compile.go
+++ b/v1/compile/compile.go
@@ -781,6 +781,27 @@ func findAnnotationsForTerm(term *ast.Term, annotationRefs []*ast.AnnotationsRef
 	return result
 }
 
+// pruneAnnotationsAndComments filters out annotations and their associated comments based on a predicate.
+// It returns the kept annotations and kept comments.
+func pruneAnnotationsAndComments(
+	module *ast.Module,
+	shouldDiscard func(*ast.Annotations) bool,
+) ([]*ast.Annotations, []*ast.Comment) {
+	keepAnnotations := slices.DeleteFunc(slices.Clone(module.Annotations), shouldDiscard)
+
+	var keepComments []*ast.Comment
+	for _, comment := range module.Comments {
+		if slices.ContainsFunc(keepAnnotations, func(a *ast.Annotations) bool {
+			return comment.Location.Row >= a.Location.Row &&
+				comment.Location.Row <= a.EndLoc().Row
+		}) {
+			keepComments = append(keepComments, comment)
+		}
+	}
+
+	return keepAnnotations, keepComments
+}
+
 // pruneBundleEntrypoints will modify modules in the provided bundle to remove
 // rules matching the entrypoints along with injecting import statements to
 // preserve their ability to compile.
@@ -816,35 +837,10 @@ func pruneBundleEntrypoints(b *bundle.Bundle, entrypointrefs []*ast.Term) error
 				}
 			}
 
-			// Drop any Annotations for rules matching the entrypoint path
-			var annotations []*ast.Annotations
-			var prunedAnnotations []*ast.Annotations
-			for _, annotation := range mf.Parsed.Annotations {
-				p := annotation.GetTargetPath()
-				// We prune annotations of dropped rules, but not packages, as the Rego file is always retained
-				if p.Equal(entrypoint.Value) && !mf.Parsed.Package.Path.Equal(entrypoint.Value) {
-					prunedAnnotations = append(prunedAnnotations, annotation)
-				} else {
-					annotations = append(annotations, annotation)
-				}
-			}
-
-			// Drop comments associated with pruned annotations
-			var comments []*ast.Comment
-			for _, comment := range mf.Parsed.Comments {
-				pruned := false
-				for _, annotation := range prunedAnnotations {
-					if comment.Location.Row >= annotation.Location.Row &&
-						comment.Location.Row <= annotation.EndLoc().Row {
-						pruned = true
-						break
-					}
-				}
-
-				if !pruned {
-					comments = append(comments, comment)
-				}
-			}
+			// Prune annotations and comments for entrypoint rules
+			annotations, comments := pruneAnnotationsAndComments(mf.Parsed, func(annotation *ast.Annotations) bool {
+				return annotation.GetTargetPath().Equal(entrypoint.Value)
+			})
 
 			// If any rules or annotations were dropped update the module accordingly
 			if len(rules) != len(mf.Parsed.Rules) || len(comments) != len(mf.Parsed.Comments) {
@@ -1215,7 +1211,15 @@ func (*optimizer) merge(a, b []bundle.ModuleFile) []bundle.ModuleFile {
 		}
 
 		if len(keep) > 0 {
+			keepAnnotations, keepComments := pruneAnnotationsAndComments(a[i].Parsed, func(annotation *ast.Annotations) bool {
+				return discarded.Contains(ast.NewTerm(annotation.GetTargetPath()))
+			})
+
 			a[i].Parsed.Rules = keep
+			a[i].Parsed.Annotations = keepAnnotations
+			a[i].Parsed.Comments = keepComments
+			// Remove the original raw source, we're editing the AST
+			// directly, so it won't be in sync anymore.
 			a[i].Raw = nil
 			b = append(b, a[i])
 		}
diff --git a/v1/compile/compile_test.go b/v1/compile/compile_test.go
index 6b605742c0..5dc9984179 100644
--- a/v1/compile/compile_test.go
+++ b/v1/compile/compile_test.go
@@ -3531,6 +3531,121 @@ func TestOptimizerOutput(t *testing.T) {
 	}
 }
 
+func TestCompilerOptimizationMultipleAnnotationEntrypoints(t *testing.T) {
+	files := map[string]string{
+		"test.rego": `package pkg
+
+# best allow rule ever
+# METADATA
+# entrypoint: true
+allow if {
+	is_admin
+	has_permission(input.action)
+}
+
+# nice deny rule
+# METADATA
+# entrypoint: true
+deny if {
+	input.user == "guest"
+	input.action == "delete"
+}
+
+# METADATA
+# description: this rule should keep its MD
+other if input.other
+
+is_admin if input.user == "admin"
+valid_actions := ["read", "write", "delete"]
+has_permission(action) if action in valid_actions
+`,
+	}
+
+	tests := []struct {
+		name            string
+		optimizationLvl int
+		expectOptimized bool
+	}{
+		{
+			name:            "optimization level 0",
+			optimizationLvl: 0,
+			expectOptimized: false,
+		},
+		{
+			name:            "optimization level 1",
+			optimizationLvl: 1,
+			expectOptimized: true,
+		},
+		{
+			name:            "optimization level 2",
+			optimizationLvl: 2,
+			expectOptimized: true,
+		},
+	}
+
+	for _, tc := range tests {
+		t.Run(tc.name, func(t *testing.T) {
+			test.WithTestFS(files, true, func(root string, fsys fs.FS) {
+				compiler := New().
+					WithFS(fsys).
+					WithPaths(root).
+					WithOptimizationLevel(tc.optimizationLvl).
+					WithRegoAnnotationEntrypoints(true)
+				err := compiler.Build(t.Context())
+				if err != nil {
+					t.Fatal(err)
+				}
+
+				// Check what the original "test.rego" remnants look like at different optimization levels
+				var originalModule *bundle.ModuleFile
+				for i := range compiler.bundle.Modules {
+					if compiler.bundle.Modules[i].Path == "test.rego" {
+						originalModule = &compiler.bundle.Modules[i]
+						break
+					}
+				}
+
+				if originalModule == nil {
+					t.Fatal("expected to find original 'test.rego' in bundle")
+				}
+
+				// The behavior differs between optimization levels
+				var expectedOriginal string
+				switch tc.optimizationLvl {
+				case 0: // At level 0, all rules remain unchanged
+					expectedOriginal = files["test.rego"]
+				case 1: // At level 1, entrypoint rules removed, is_admin and has_permission inlined
+					expectedOriginal = `package pkg
+
+# METADATA
+# description: this rule should keep its MD
+other if input.other
+
+valid_actions := ["read", "write", "delete"]
+`
+				case 2: // At level 2, entrypoint rules removed, support rules preserved
+					expectedOriginal = `package pkg
+
+# METADATA
+# description: this rule should keep its MD
+other if input.other
+
+is_admin if input.user == "admin"
+valid_actions := ["read", "write", "delete"]
+has_permission(action) if action in valid_actions
+`
+				}
+
+				actualOriginal := string(originalModule.Raw)
+				if actualOriginal != expectedOriginal {
+					t.Errorf("original module mismatch at level %d:\n\nexpected:\n%s\n\ngot:\n%s",
+						tc.optimizationLvl, expectedOriginal, actualOriginal)
+				}
+			})
+		})
+	}
+}
+
 func TestOptimizerError(t *testing.T) {
 	tests := []struct {
 		note        string