diff --git a/CHANGES.md b/CHANGES.md
index ed69b0eaf7e..65a450604d6 100644
--- a/CHANGES.md
+++ b/CHANGES.md
@@ -29,6 +29,9 @@
 - `coqdep` now depends only on the filesystem layout of the .v files,
   and not on their contents (#5547, helps with #5100, @ejgallego)
 
+- The mdx stanza 0.2 can now be used with `(implicit_transitive_deps false)`
+  (#5558, fixes #5499, @emillon)
+
 3.0.3 (Unreleased)
 ------------------
 
diff --git a/src/dune_rules/mdx.ml b/src/dune_rules/mdx.ml
index 616e9d3a922..7e789c6bd60 100644
--- a/src/dune_rules/mdx.ml
+++ b/src/dune_rules/mdx.ml
@@ -312,10 +312,11 @@ let mdx_prog_gen t ~sctx ~dir ~scope ~expander ~mdx_prog =
   let module_ = Module.generated ~src_dir:(Path.build dir) main_module_name in
   let modules = Modules.singleton_exe module_ in
   let flags = Ocaml_flags.default ~dune_version ~profile:Release in
+  let lib name = Lib_dep.Direct (loc, Lib_name.of_string name) in
   let compile_info =
     Lib.DB.resolve_user_written_deps_for_exes (Scope.libs scope)
       [ (t.loc, name) ]
-      (Lib_dep.Direct (loc, Lib_name.of_string "mdx.test") :: t.libraries)
+      (lib "mdx.test" :: lib "mdx.top" :: t.libraries)
       ~pps:[] ~dune_version
   in
   let* cctx =
diff --git a/test/blackbox-tests/test-cases/mdx-stanza/implicit-transitive-deps-false.t b/test/blackbox-tests/test-cases/mdx-stanza/implicit-transitive-deps-false.t
index bb292de5876..1c381633709 100644
--- a/test/blackbox-tests/test-cases/mdx-stanza/implicit-transitive-deps-false.t
+++ b/test/blackbox-tests/test-cases/mdx-stanza/implicit-transitive-deps-false.t
@@ -1,6 +1,5 @@
-Building the executable generated by the MDX stanza fails when implicit
-transitive dependencies are disabled due to an implicit dependency on the
-`mdx.top` library:
+Building the executable generated by the MDX stanza works when implicit
+transitive dependencies are disabled.
 
   $ cat >dune-project <<EOF
   > (lang dune 3.0)
@@ -13,19 +12,3 @@ transitive dependencies are disabled due to an implicit dependency on the
   > EOF
 
   $ dune build
-  File "mdx_gen.ml-gen", line 28, characters 2-19:
-  28 |   Mdx_top.Directory path) []
-         ^^^^^^^^^^^^^^^^^
-  Error: Unbound module Mdx_top
-  [1]
-
-Adding `mdx.top` as an explicit dependency of the stanza fixes the issue:
-
-  $ cat >dune <<EOF
-  > (mdx
-  >  (files markdown_file.md)
-  >  (libraries mdx.top))
-  > EOF
-
-  $ dune build
-