diff --git a/src/ir/metadata.cpp b/src/ir/metadata.cpp
index a260ade165b..6ac749b1fff 100644
--- a/src/ir/metadata.cpp
+++ b/src/ir/metadata.cpp
@@ -44,7 +44,8 @@ void copyBetweenFunctions(Expression* origin,
                           Function* originFunc,
                           Function* copyFunc) {
   if (originFunc->debugLocations.empty() &&
-      originFunc->codeAnnotations.empty()) {
+      originFunc->codeAnnotations.empty() &&
+      originFunc->funcAnnotations.empty()) {
     // Nothing to copy.
     return;
   }
@@ -75,7 +76,7 @@ void copyBetweenFunctions(Expression* origin,
     }
   }
 
-  // Also copy function-level annotations, if any.
+  // Also copy function-level annotations.
   copyFunc->funcAnnotations = originFunc->funcAnnotations;
 }
 
diff --git a/src/wasm.h b/src/wasm.h
index 2731986bde5..3c84e02b984 100644
--- a/src/wasm.h
+++ b/src/wasm.h
@@ -2279,6 +2279,9 @@ struct CodeAnnotation {
     return removableIfUnused == other.removableIfUnused &&
            jsCalled == other.jsCalled && idempotent == other.idempotent;
   }
+
+  // Checks if no annotation is actually set.
+  bool empty() { return *this == CodeAnnotation(); }
 };
 
 class Function : public Importable {
diff --git a/test/lit/merge/annotations-func-only.wat b/test/lit/merge/annotations-func-only.wat
new file mode 100644
index 00000000000..90f01d08362
--- /dev/null
+++ b/test/lit/merge/annotations-func-only.wat
@@ -0,0 +1,44 @@
+;; NOTE: Assertions have been generated by update_lit_checks.py --all-items and should not be edited.
+
+;; RUN: wasm-merge %s first %s.second second -all -S -o - | filecheck %s
+
+;; Test that we handle code annotations properly when they appear *only* in
+;; functions (not code). Both the first and second wasm files have an annotation
+;; that should be preserved.
+
+(module
+  ;; CHECK:      (type $0 (func))
+
+  ;; CHECK:      (export "first" (func $first))
+
+  ;; CHECK:      (export "second" (func $second))
+
+  ;; CHECK:      (@binaryen.js.called)
+  ;; CHECK-NEXT: (func $first (type $0)
+  ;; CHECK-NEXT:  (if
+  ;; CHECK-NEXT:   (i32.const 0)
+  ;; CHECK-NEXT:   (then
+  ;; CHECK-NEXT:    (return)
+  ;; CHECK-NEXT:   )
+  ;; CHECK-NEXT:  )
+  ;; CHECK-NEXT: )
+  (@binaryen.js.called)
+  (func $first (export "first")
+    (if
+      (i32.const 0)
+      (then
+        (return)
+      )
+    )
+  )
+)
+
+;; CHECK:      (@binaryen.js.called)
+;; CHECK-NEXT: (func $second (type $0)
+;; CHECK-NEXT:  (if
+;; CHECK-NEXT:   (i32.const 0)
+;; CHECK-NEXT:   (then
+;; CHECK-NEXT:    (return)
+;; CHECK-NEXT:   )
+;; CHECK-NEXT:  )
+;; CHECK-NEXT: )
diff --git a/test/lit/merge/annotations-func-only.wat.second b/test/lit/merge/annotations-func-only.wat.second
new file mode 100644
index 00000000000..2bc67fd5c0e
--- /dev/null
+++ b/test/lit/merge/annotations-func-only.wat.second
@@ -0,0 +1,12 @@
+(module
+  (@binaryen.js.called)
+  (func $second (export "second")
+    (if
+      (i32.const 0)
+      (then
+        (return)
+      )
+    )
+  )
+)
+