diff --git a/src/builder-manifest.c b/src/builder-manifest.c
index 9304587d..2c275131 100644
--- a/src/builder-manifest.c
+++ b/src/builder-manifest.c
@@ -2783,6 +2783,22 @@ builder_manifest_cleanup (BuilderManifest *self,
             }
         }
 
+      if (builder_context_get_separate_locales (context))
+        {
+          g_autoptr(GFile) root_dir = NULL;
+
+          if (builder_context_get_build_runtime (context))
+            root_dir = g_file_get_child (app_dir, "usr");
+          else
+            root_dir = g_file_get_child (app_dir, "files");
+
+          if (!builder_migrate_locale_dirs (root_dir, error))
+            {
+              g_prefix_error (error, "Can't migrate locale dirs: ");
+              return FALSE;
+            }
+        }
+
       app_root = g_file_get_child (app_dir, "files");
 
       appdata_source = builder_manifest_find_appdata_file (self, app_root);
diff --git a/src/builder-module.c b/src/builder-module.c
index d1a7aa55..8d5d92b5 100644
--- a/src/builder-module.c
+++ b/src/builder-module.c
@@ -2178,22 +2178,6 @@ builder_module_build_helper (BuilderModule   *self,
         return FALSE;
     }
 
-  if (builder_context_get_separate_locales (context))
-    {
-      g_autoptr(GFile) root_dir = NULL;
-
-      if (builder_context_get_build_runtime (context))
-        root_dir = g_file_get_child (app_dir, "usr");
-      else
-        root_dir = g_file_get_child (app_dir, "files");
-
-      if (!builder_migrate_locale_dirs (root_dir, error))
-        {
-          g_prefix_error (error, "module %s: ", self->name);
-          return FALSE;
-        }
-    }
-
   if (!builder_module_install_licenses (self, id, source_dir, app_dir, error))
     return FALSE;
 
diff --git a/tests/meson.build b/tests/meson.build
index c1fda2cb..2addf09e 100644
--- a/tests/meson.build
+++ b/tests/meson.build
@@ -123,6 +123,7 @@ if get_option('installed_tests')
     'org.flatpak.appstream_media.json',
     'org.test.Hello-256.png',
     'org.flatpak.install_test.json',
+    'test-locale-cleanup.json',
 
     install_dir: installed_testdir,
     install_mode: 'rw-r--r--',
diff --git a/tests/test-builder.sh b/tests/test-builder.sh
index 16407856..13792a26 100755
--- a/tests/test-builder.sh
+++ b/tests/test-builder.sh
@@ -23,7 +23,7 @@ set -euo pipefail
 
 skip_without_fuse
 
-echo "1..11"
+echo "1..12"
 
 setup_repo
 install_repo
@@ -56,6 +56,7 @@ cp $(dirname $0)/org.test.Hello.png .
 cp $(dirname $0)/org.test.Hello-256.png .
 cp $(dirname $0)/org.flatpak.appstream_media.json .
 cp $(dirname $0)/org.flatpak.install_test.json .
+cp $(dirname $0)/test-locale-cleanup.json .
 mkdir include1
 cp $(dirname $0)/module1.json include1/
 cp $(dirname $0)/module1.yaml include1/
@@ -184,3 +185,10 @@ echo "$REFS" | grep -q "org\.flatpak\.install_test\.Debug"
 echo "$REFS" | grep -q "org\.flatpak\.install_test\.Locale"
 
 echo "ok install"
+
+${FLATPAK_BUILDER} --repo=$REPO --force-clean appdir test-locale-cleanup.json >&2
+
+assert_not_has_file appdir/files/share/runtime/locale/es/share/es/testA.mo
+assert_has_file appdir/files/share/runtime/locale/es/share/es/testB.mo
+
+echo "ok testB's locale survives after testA's cleanup"
diff --git a/tests/test-locale-cleanup.json b/tests/test-locale-cleanup.json
new file mode 100644
index 00000000..6ef36e26
--- /dev/null
+++ b/tests/test-locale-cleanup.json
@@ -0,0 +1,26 @@
+{
+    "app-id": "org.test.LocaleCleanup",
+    "runtime": "org.test.Platform",
+    "sdk": "org.test.Sdk",
+    "modules": [
+        {
+            "name": "testA",
+            "cleanup": [
+                "/share/locale"
+            ],
+            "buildsystem": "simple",
+            "build-commands": [
+                "mkdir -p /app/share/locale/es",
+                "touch /app/share/locale/es/testA.mo"
+            ]
+        },
+        {
+            "name": "testB",
+            "buildsystem": "simple",
+            "build-commands": [
+                "mkdir -p /app/share/locale/es",
+                "touch /app/share/locale/es/testB.mo"
+            ]
+        }
+    ]
+}