diff --git a/src/dir_contents.ml b/src/dir_contents.ml
index 5401b8a3..8eb1aa3c 100644
--- a/src/dir_contents.ml
+++ b/src/dir_contents.ml
@@ -197,7 +197,8 @@ end = struct
       | Simple true -> (wrap_modules modules, Module.Name.Map.empty)
       | Yes_with_transition _ ->
         ( wrap_modules modules
-        , Module.Name.Map.map ~f:Module.deprecate modules
+        , Module.Name.Map.remove modules main_module_name
+          |> Module.Name.Map.map ~f:Module.deprecate
         )
     in
     let alias_module =
diff --git a/test/blackbox-tests/test-cases/wrapped-transition/lib/mylib.ml b/test/blackbox-tests/test-cases/wrapped-transition/lib/mylib.ml
new file mode 100644
index 00000000..54287077
--- /dev/null
+++ b/test/blackbox-tests/test-cases/wrapped-transition/lib/mylib.ml
@@ -0,0 +1,3 @@
+module Bar = Bar
+module Foo = Foo
+module Intf_only = Intf_only