diff --git a/Source/Core/DolphinNoGUI/MainNoGUI.cpp b/Source/Core/DolphinNoGUI/MainNoGUI.cpp
index 11bbf55da1..71d8960652 100644
--- a/Source/Core/DolphinNoGUI/MainNoGUI.cpp
+++ b/Source/Core/DolphinNoGUI/MainNoGUI.cpp
@@ -251,6 +251,10 @@ int main(int argc, char* argv[])
   if (options.is_set("user"))
     user_directory = static_cast<const char*>(options.get("user"));
 
+  UICommon::SetUserDirectory(user_directory);
+  UICommon::Init();
+  GCAdapter::Init();
+
   s_platform = GetPlatform(options);
   if (!s_platform || !s_platform->Init())
   {
@@ -258,17 +262,6 @@ int main(int argc, char* argv[])
     return 1;
   }
 
-  const WindowSystemInfo wsi = s_platform->GetWindowSystemInfo();
-
-  UICommon::SetUserDirectory(user_directory);
-  UICommon::Init();
-  UICommon::InitControllers(wsi);
-
-  Common::ScopeGuard ui_common_guard([] {
-    UICommon::ShutdownControllers();
-    UICommon::Shutdown();
-  });
-
   if (save_state_path && !game_specified)
   {
     fprintf(stderr, "A save state cannot be loaded without specifying a game to launch.\n");
@@ -295,7 +288,7 @@ int main(int argc, char* argv[])
 
   DolphinAnalytics::Instance().ReportDolphinStart("nogui");
 
-  if (!BootManager::BootCore(std::move(boot), wsi))
+  if (!BootManager::BootCore(std::move(boot), s_platform->GetWindowSystemInfo()))
   {
     fprintf(stderr, "Could not boot the specified file\n");
     return 1;
@@ -310,6 +303,7 @@ int main(int argc, char* argv[])
 
   Core::Shutdown();
   s_platform.reset();
+  UICommon::Shutdown();
 
   return 0;
 }

diff --git a/Source/Core/Core/Core.cpp b/Source/Core/Core/Core.cpp
index 8a02534c57..00d8ac09e8 100644
--- a/Source/Core/Core/Core.cpp
+++ b/Source/Core/Core/Core.cpp
@@ -470,14 +470,26 @@ static void EmuThread(std::unique_ptr<BootParameters> boot, WindowSystemInfo wsi
   DeclareAsCPUThread();
   s_frame_step = false;

-  // Switch the window used for inputs to the render window. This way, the cursor position
-  // is relative to the render window, instead of the main window.
-  ASSERT(g_controller_interface.IsInit());
-  g_controller_interface.ChangeWindow(wsi.render_window);
-
-  Pad::LoadConfig();
-  Pad::LoadGBAConfig();
-  Keyboard::LoadConfig();
+  // The frontend will likely have initialized the controller interface, as it needs
+  // it to provide the configuration dialogs. In this case, instead of re-initializing
+  // entirely, we switch the window used for inputs to the render window. This way, the
+  // cursor position is relative to the render window, instead of the main window.
+  bool init_controllers = false;
+  if (!g_controller_interface.IsInit())
+  {
+    g_controller_interface.Initialize(wsi);
+    Pad::Initialize();
+    Pad::InitializeGBA();
+    Keyboard::Initialize();
+    init_controllers = true;
+  }
+  else
+  {
+    g_controller_interface.ChangeWindow(wsi.render_window);
+    Pad::LoadConfig();
+    Pad::LoadGBAConfig();
+    Keyboard::LoadConfig();
+  }

   BootSessionData boot_session_data = std::move(boot->boot_session_data);
   const std::optional<std::string>& savestate_path = boot_session_data.GetSavestatePath();
@@ -494,13 +506,50 @@ static void EmuThread(std::unique_ptr<BootParameters> boot, WindowSystemInfo wsi
       Common::SyncSDImageToSDFolder();
   }};

-  // Load Wiimotes - only if we are booting in Wii mode
+  // Load and Init Wiimotes - only if we are booting in Wii mode
+  bool init_wiimotes = false;
   if (core_parameter.bWii && !Config::Get(Config::MAIN_BLUETOOTH_PASSTHROUGH_ENABLED))
   {
-    Wiimote::LoadConfig();
+    if (init_controllers)
+    {
+      Wiimote::Initialize(savestate_path ? Wiimote::InitializeMode::DO_WAIT_FOR_WIIMOTES :
+                                           Wiimote::InitializeMode::DO_NOT_WAIT_FOR_WIIMOTES);
+      init_wiimotes = true;
+    }
+    else
+    {
+      Wiimote::LoadConfig();
+    }
   }

-  FreeLook::LoadInputConfig();
+  if (init_controllers)
+  {
+    FreeLook::Initialize();
+  }
+  else
+  {
+    FreeLook::LoadInputConfig();
+  }
+
+  Common::ScopeGuard controller_guard{[init_controllers, init_wiimotes] {
+    if (!init_controllers)
+      return;
+
+    if (init_wiimotes)
+    {
+      Wiimote::ResetAllWiimotes();
+      Wiimote::Shutdown();
+    }
+
+    FreeLook::Shutdown();
+
+    ResetRumble();
+
+    Keyboard::Shutdown();
+    Pad::Shutdown();
+    Pad::ShutdownGBA();
+    g_controller_interface.Shutdown();
+  }};

   Movie::Init(*boot);
   Common::ScopeGuard movie_guard{&Movie::Shutdown};