diff --git a/doc/changes/12299.md b/doc/changes/12299.md
new file mode 100644
index 00000000000..f0371ef86cd
--- /dev/null
+++ b/doc/changes/12299.md
@@ -0,0 +1,2 @@
+- Fix: include the module alias in the transitive dependency closure with
+  `(include_subdirs qualified). (#12299, @anmonteiro)
diff --git a/src/dune_rules/modules.ml b/src/dune_rules/modules.ml
index 526b54110ab..c952c7abbf9 100644
--- a/src/dune_rules/modules.ml
+++ b/src/dune_rules/modules.ml
@@ -453,7 +453,10 @@ module Group = struct
         (* XXX ocamldep can't currently give us precise dependencies for
            modules under [(include_subdirs qualified)] directories. For that
            reason we currently depend on everything under the sub-directory. *)
-        Module_name.Map.values g.modules |> List.concat_map ~f:closure_node
+        let closure =
+          Module_name.Map.values g.modules |> List.concat_map ~f:closure_node
+        in
+        lib_interface :: closure
       | _ -> [ lib_interface ]
 
     and closure_node = function
diff --git a/test/blackbox-tests/test-cases/include-qualified/build-with-sandbox.t b/test/blackbox-tests/test-cases/include-qualified/build-with-sandbox.t
new file mode 100644
index 00000000000..f305b144cac
--- /dev/null
+++ b/test/blackbox-tests/test-cases/include-qualified/build-with-sandbox.t
@@ -0,0 +1,28 @@
+Test `(include_subdirs qualified)` with sandboxing
+
+  $ mkdir lib
+  $ cat > dune-project <<EOF
+  > (lang dune 3.20)
+  > EOF
+
+  $ mkdir lib/sub
+  $ cat > lib/dune <<EOF
+  > (include_subdirs qualified)
+  > (library (name foo))
+  > EOF
+  $ cat > lib/bar.ml <<EOF
+  > let hello = Sub.Hello.hello
+  > EOF
+  $ cat > lib/sub/hello.ml <<EOF
+  > let hello = "hello from sub"
+  > EOF
+
+  $ DUNE_SANDBOX=symlink dune build
+
+Transitive deps file includes the alias module
+
+  $ cat _build/default/lib/.foo.objs/foo__Bar.impl.d
+  lib/bar.ml: Sub
+  $ cat _build/default/lib/.foo.objs/foo__Bar.impl.all-deps
+  foo__Sub
+  foo__Sub__Hello