diff --git a/src/yuzu/main.cpp b/src/yuzu/main.cpp
index 2ac8344a3..68ad43a80 100644
--- a/src/yuzu/main.cpp
+++ b/src/yuzu/main.cpp
@@ -295,6 +295,10 @@ void GMainWindow::ControllerSelectorReconfigureControllers(
 
     emit ControllerSelectorReconfigureFinished();
 
+    // Don't forget to apply settings.
+    Settings::Apply();
+    config->Save();
+
     UpdateStatusButtons();
 }