diff --git a/doc/changes/12464.md b/doc/changes/12464.md
new file mode 100644
index 00000000000..c23a8ec33ad
--- /dev/null
+++ b/doc/changes/12464.md
@@ -0,0 +1,2 @@
+- melange support: don't emit empty JavaScript modules for generated module
+  aliases. (#12464, @anmonteiro)
diff --git a/src/dune_rules/melange/melange_rules.ml b/src/dune_rules/melange/melange_rules.ml
index bbd98d0246e..d16616471bd 100644
--- a/src/dune_rules/melange/melange_rules.ml
+++ b/src/dune_rules/melange/melange_rules.ml
@@ -127,9 +127,14 @@ let impl_only_modules_defined_in_this_lib ~sctx ~scope lib =
           ]
       | true -> ()
     in
-    ( modules
-    , (Modules.With_vlib.split_by_lib modules).impl
-      |> List.filter ~f:(Module.has ~ml_kind:Impl) )
+    let impl_only =
+      Modules.With_vlib.fold_no_vlib_with_aliases
+        modules
+        ~init:[]
+        ~normal:(fun m acc -> if Module.has m ~ml_kind:Impl then m :: acc else acc)
+        ~alias:(fun _m acc -> acc)
+    in
+    modules, impl_only
 ;;
 
 let cmj_includes =
@@ -183,13 +188,15 @@ let compile_info ~scope (mel : Melange_stanzas.Emit.t) =
 let js_targets_of_modules modules ~module_systems ~output =
   List.map module_systems ~f:(fun (_, js_ext) ->
     modules
-    |> Modules.With_vlib.drop_vlib
-    |> Modules.fold_user_available ~init:Path.Set.empty ~f:(fun m acc ->
-      if Module.has m ~ml_kind:Impl
-      then (
-        let target = Path.build @@ make_js_name ~js_ext ~output m in
-        Path.Set.add acc target)
-      else acc))
+    |> Modules.With_vlib.fold_no_vlib_with_aliases
+         ~init:Path.Set.empty
+         ~alias:(fun _m acc -> acc)
+         ~normal:(fun m acc ->
+           if Module.has m ~ml_kind:Impl
+           then (
+             let target = Path.build @@ make_js_name ~js_ext ~output m in
+             Path.Set.add acc target)
+           else acc))
   |> Path.Set.union_all
 ;;
 
diff --git a/test/blackbox-tests/test-cases/melange/emit-private.t b/test/blackbox-tests/test-cases/melange/emit-private.t
index d71b031e501..db5c78a4147 100644
--- a/test/blackbox-tests/test-cases/melange/emit-private.t
+++ b/test/blackbox-tests/test-cases/melange/emit-private.t
@@ -47,7 +47,6 @@ Test dependency on a private library in the same package as melange.emit
   > EOF
 
   $ OCAMLPATH=$PWD/prefix/lib/:$OCAMLPATH dune build @dist --display=short 2>&1 | grep -v melange
-          melc b/dist/node_modules/pkg.__private__.a/a.js
           melc b/dist/node_modules/pkg.__private__.a/foo.js
           melc b/dist/b/bar.js
 
diff --git a/test/blackbox-tests/test-cases/melange/empty-aliases-file.t b/test/blackbox-tests/test-cases/melange/empty-aliases-file.t
new file mode 100644
index 00000000000..7f6d33f0572
--- /dev/null
+++ b/test/blackbox-tests/test-cases/melange/empty-aliases-file.t
@@ -0,0 +1,129 @@
+
+  $ mkdir lib
+  $ cat > dune-project <<EOF
+  > (lang dune 3.20)
+  > (package (name foo))
+  > (using melange 1.0)
+  > EOF
+
+  $ cat > lib/dune <<EOF
+  > (library
+  >  (name foo)
+  >  (modes melange))
+  > EOF
+  $ cat > lib/bar.ml <<EOF
+  > let greeting = "hello"
+  > EOF
+
+  $ cat > dune <<EOF
+  > (melange.emit
+  >  (target dist)
+  >  (libraries foo)
+  >  (emit_stdlib false)
+  >  (modules))
+  > EOF
+  $ cat > lib/bar.ml <<EOF
+  > let greeting = "hello"
+  > EOF
+
+  $ dune build @melange
+
+No `.js` file present for the library alias `foo.js`
+
+  $ find _build/default/dist/lib -type f | sort
+  _build/default/dist/lib/bar.js
+
+Now write a foo.ml file
+
+  $ cat > lib/dune <<EOF
+  > (library
+  >  (name foo)
+  >  (modes melange))
+  > EOF
+  $ cat > lib/foo.ml <<EOF
+  > module Bar = Bar
+  > let x = "foo"
+  > EOF
+
+  $ dune build @melange
+
+`foo.js` was manually written, therefore it's present
+
+  $ find _build/default/dist/ -type f | sort
+  _build/default/dist/lib/bar.js
+  _build/default/dist/lib/foo.js
+  $ cat _build/default/dist/lib/foo.js
+  // Generated by Melange
+  'use strict';
+  
+  
+  const x = "foo";
+  
+  module.exports = {
+    x,
+  }
+  /* No side effect */
+
+`(include_subdirs qualified)`
+
+  $ mkdir lib/sub
+  $ cat > lib/dune <<EOF
+  > (include_subdirs qualified)
+  > (library
+  >  (name foo)
+  >  (modes melange))
+  > EOF
+  $ cat > lib/bar.ml <<EOF
+  > let hello = Sub.Hello.hello
+  > EOF
+  $ cat > lib/sub/hello.ml <<EOF
+  > let hello = "hello from sub"
+  > EOF
+  $ cat > lib/foo.ml <<EOF
+  > module Bar = Bar
+  > let x = "foo"
+  > EOF
+
+  $ dune build @melange
+
+`foo.js` was manually written, therefore it's present. `sub.js` is an alias
+file, and it's not present
+
+  $ find _build/default/dist/lib -type f | sort
+  _build/default/dist/lib/bar.js
+  _build/default/dist/lib/foo.js
+  _build/default/dist/lib/sub/hello.js
+
+  $ cat > lib/dune <<EOF
+  > (include_subdirs qualified)
+  > (library
+  >  (name foo)
+  >  (modes melange))
+  > EOF
+  $ cat > lib/bar.ml <<EOF
+  > let hello = Sub.Hello.hello ^ Sub.world
+  > EOF
+  $ cat > lib/sub/sub.ml <<EOF
+  > module Hello = Hello
+  > let world = "world"
+  > EOF
+  $ cat > lib/sub/hello.ml <<EOF
+  > let hello = "hello from sub"
+  > EOF
+  $ cat > lib/foo.ml <<EOF
+  > module Bar = Bar
+  > let x = "foo"
+  > EOF
+
+  $ DUNE_SANDBOX=none dune build @melange
+
+`foo.js` was manually written, therefore it's present. `sub.js` is an alias
+file, and it's not present
+
+  $ find _build/default/dist/lib -type f | sort
+  _build/default/dist/lib/bar.js
+  _build/default/dist/lib/foo.js
+  _build/default/dist/lib/sub/hello.js
+  _build/default/dist/lib/sub/sub.js
+
+
diff --git a/test/blackbox-tests/test-cases/melange/include_subdirs.t/run.t b/test/blackbox-tests/test-cases/melange/include_subdirs.t/run.t
index 50100d906db..c5962a2fb0e 100644
--- a/test/blackbox-tests/test-cases/melange/include_subdirs.t/run.t
+++ b/test/blackbox-tests/test-cases/melange/include_subdirs.t/run.t
@@ -10,7 +10,6 @@ source:
 
   $ find _build/default/$output -iname "*.js" | grep -v melange | sort
   _build/default/inside/output/inside/app/b.js
-  _build/default/inside/output/inside/app/lib.js
   _build/default/inside/output/inside/app/lib/a.js
   _build/default/inside/output/inside/c.js
   $ node _build/default/$output/inside/c.js