diff --git a/source/blender/windowmanager/intern/wm_files.c b/source/blender/windowmanager/intern/wm_files.c
index 31af7804058..efbc0d78754 100644
--- a/source/blender/windowmanager/intern/wm_files.c
+++ b/source/blender/windowmanager/intern/wm_files.c
@@ -526,6 +526,17 @@ int wm_homefile_read(bContext *C, ReportList *reports, bool from_memory, const c
 	char prefstr[FILE_MAX];
 	int success = 0;
 
+	/* Indicates whether file was really load from memory.
+	 *
+	 * This is used for versioning code, and for this we can not rely on from_memory
+	 * passed via argument. This is because there might be configuration folder
+	 * exists but it might not have startup.blend and in this case we fallback to
+	 * reading home file from memory.
+	 *
+	 * And in this case versioning code is to be run.
+	 */
+	bool read_file_from_memory = false;
+
 	/* options exclude eachother */
 	BLI_assert((from_memory && custom_file) == 0);
 
@@ -578,6 +589,7 @@ int wm_homefile_read(bContext *C, ReportList *reports, bool from_memory, const c
 	}
 
 	if (success == 0) {
+		read_file_from_memory = true;
 		success = BKE_read_file_from_memory(C, datatoc_startup_blend, datatoc_startup_blend_size, NULL, true);
 		if (wmbase.first == NULL) wm_clear_default_size(C);
 		BLI_init_temporary_dir(U.tempdir);
@@ -600,7 +612,7 @@ int wm_homefile_read(bContext *C, ReportList *reports, bool from_memory, const c
 	G.fileflags &= ~G_FILE_RELATIVE_REMAP;
 	
 	/* check userdef before open window, keymaps etc */
-	wm_init_userdef(C, (bool)from_memory);
+	wm_init_userdef(C, read_file_from_memory);
 	
 	/* match the read WM with current WM */
 	wm_window_match_do(C, &wmbase);