diff --git a/src/rebar_core.erl b/src/rebar_core.erl
index 1313c7f..ceb3d3c 100644
--- a/src/rebar_core.erl
+++ b/src/rebar_core.erl
@@ -124,8 +124,8 @@ maybe_process_dir({[], undefined}=ModuleSet, Config, CurrentCodePath,
     process_dir0(Dir, Command, DirSet, Config, CurrentCodePath, ModuleSet);
 maybe_process_dir({_, ModuleSetFile}=ModuleSet, Config, CurrentCodePath,
                   Dir, Command, DirSet) ->
-    case lists:suffix(".app", ModuleSetFile)
-        orelse lists:suffix(".app.src", ModuleSetFile) of
+    case lists:suffix(".app.src", ModuleSetFile)
+        orelse lists:suffix(".app", ModuleSetFile) of
         true ->
             %% .app or .app.src file, check if is_skipped_app
             maybe_process_dir0(ModuleSetFile, ModuleSet,