diff --git a/CHANGES b/CHANGES
index cfdff2aba..3feb26d4f 100644
--- a/CHANGES
+++ b/CHANGES
@@ -35,6 +35,7 @@ Bugfixes:
  - Qt: Fix controllers sometimes not loading the right profile
 Misc:
  - Qt: Show multiplayer numbers in window title
+ - Qt: Handle saving input settings better
 
 0.2.0: (2015-04-03)
 Features:
diff --git a/src/gba/input.c b/src/gba/input.c
index 439a11d36..97b5c9103 100644
--- a/src/gba/input.c
+++ b/src/gba/input.c
@@ -505,9 +505,12 @@ const char* GBAInputGetCustomValue(const struct Configuration* config, uint32_t
 	char sectionName[SECTION_NAME_MAX];
 	if (profile) {
 		snprintf(sectionName, SECTION_NAME_MAX, "input-profile.%s", profile);
-	} else {
-		_makeSectionName(sectionName, SECTION_NAME_MAX, type);
+		const char* value = ConfigurationGetValue(config, sectionName, key);
+		if (value) {
+			return value;
+		}
 	}
+	_makeSectionName(sectionName, SECTION_NAME_MAX, type);
 	return ConfigurationGetValue(config, sectionName, key);
 }
 
@@ -515,8 +518,8 @@ void GBAInputSetCustomValue(struct Configuration* config, uint32_t type, const c
 	char sectionName[SECTION_NAME_MAX];
 	if (profile) {
 		snprintf(sectionName, SECTION_NAME_MAX, "input-profile.%s", profile);
-	} else {
-		_makeSectionName(sectionName, SECTION_NAME_MAX, type);
+		ConfigurationSetValue(config, sectionName, key, value);
 	}
+	_makeSectionName(sectionName, SECTION_NAME_MAX, type);
 	ConfigurationSetValue(config, sectionName, key, value);
 }
diff --git a/src/platform/qt/ConfigController.cpp b/src/platform/qt/ConfigController.cpp
index 9857727d8..ff6fd9664 100644
--- a/src/platform/qt/ConfigController.cpp
+++ b/src/platform/qt/ConfigController.cpp
@@ -120,8 +120,6 @@ ConfigController::ConfigController(QObject* parent)
 }
 
 ConfigController::~ConfigController() {
-	write();
-
 	GBAConfigDeinit(&m_config);
 	GBAConfigFreeOpts(&m_opts);
 }
diff --git a/src/platform/qt/InputController.cpp b/src/platform/qt/InputController.cpp
index 9dfb58daf..e72e7f2b9 100644
--- a/src/platform/qt/InputController.cpp
+++ b/src/platform/qt/InputController.cpp
@@ -108,13 +108,20 @@ void InputController::loadProfile(uint32_t type, const QString& profile) {
 #endif
 }
 
-void InputController::saveConfiguration(uint32_t type) {
-	GBAInputMapSave(&m_inputMap, type, m_config->input());
+void InputController::saveConfiguration() {
+	saveConfiguration(KEYBOARD);
 #ifdef BUILD_SDL
+	saveConfiguration(SDL_BINDING_BUTTON);
+	saveProfile(SDL_BINDING_BUTTON, profileForType(SDL_BINDING_BUTTON));
 	if (m_playerAttached) {
 		GBASDLPlayerSaveConfig(&m_sdlPlayer, m_config->input());
 	}
+	m_config->write();
 #endif
+}
+
+void InputController::saveConfiguration(uint32_t type) {
+	GBAInputMapSave(&m_inputMap, type, m_config->input());
 	m_config->write();
 }
 
diff --git a/src/platform/qt/InputController.h b/src/platform/qt/InputController.h
index b4a73bab1..175445e3e 100644
--- a/src/platform/qt/InputController.h
+++ b/src/platform/qt/InputController.h
@@ -36,9 +36,10 @@ public:
 	~InputController();
 
 	void setConfiguration(ConfigController* config);
+	void saveConfiguration();
 	void loadConfiguration(uint32_t type);
 	void loadProfile(uint32_t type, const QString& profile);
-	void saveConfiguration(uint32_t type = KEYBOARD);
+	void saveConfiguration(uint32_t type);
 	void saveProfile(uint32_t type, const QString& profile);
 	const char* profileForType(uint32_t type);
 
diff --git a/src/platform/qt/Window.cpp b/src/platform/qt/Window.cpp
index 6984fb7e2..df434575a 100644
--- a/src/platform/qt/Window.cpp
+++ b/src/platform/qt/Window.cpp
@@ -197,6 +197,7 @@ void Window::loadConfig() {
 }
 
 void Window::saveConfig() {
+	m_inputController.saveConfiguration();
 	m_config->write();
 }
 
@@ -411,6 +412,7 @@ void Window::resizeEvent(QResizeEvent*) {
 void Window::closeEvent(QCloseEvent* event) {
 	emit shutdown();
 	m_config->setQtOption("windowPos", pos());
+	saveConfig();
 	QMainWindow::closeEvent(event);
 }