diff --git a/Source/Core/DolphinQt/Config/GamecubeControllersWidget.cpp b/Source/Core/DolphinQt/Config/GamecubeControllersWidget.cpp
index c27ab2e99f..38ea1e4e7f 100644
--- a/Source/Core/DolphinQt/Config/GamecubeControllersWidget.cpp
+++ b/Source/Core/DolphinQt/Config/GamecubeControllersWidget.cpp
@@ -198,12 +198,11 @@ void GamecubeControllersWidget::SaveSettings()
                                                                       static_cast<s32>(i));
       }
     }
-
-    if (GCAdapter::UseAdapter())
-      GCAdapter::StartScanThread();
-    else
-      GCAdapter::StopScanThread();
   }
+  if (GCAdapter::UseAdapter())
+    GCAdapter::StartScanThread();
+  else
+    GCAdapter::StopScanThread();
 
   SConfig::GetInstance().SaveSettings();
 }
diff --git a/Source/Core/InputCommon/GCAdapter.cpp b/Source/Core/InputCommon/GCAdapter.cpp
index a3853e9e6c..ec3c3a1fb3 100644
--- a/Source/Core/InputCommon/GCAdapter.cpp
+++ b/Source/Core/InputCommon/GCAdapter.cpp
@@ -203,14 +203,25 @@ static void ReadThreadFunc()
     std::array<u8, CONTROLER_INPUT_PAYLOAD_EXPECTED_SIZE> input_buffer;
 
     int payload_size = 0;
-    const int error =
-        libusb_interrupt_transfer(s_handle, s_endpoint_in, input_buffer.data(),
-                                  int(input_buffer.size()), &payload_size, USB_TIMEOUT_MS);
+    int error = libusb_interrupt_transfer(s_handle, s_endpoint_in, input_buffer.data(),
+                                          int(input_buffer.size()), &payload_size, USB_TIMEOUT_MS);
     if (error != LIBUSB_SUCCESS)
     {
       ERROR_LOG_FMT(CONTROLLERINTERFACE, "Read: libusb_interrupt_transfer failed: {}",
                     LibusbUtils::ErrorWrap(error));
     }
+    if (error == LIBUSB_ERROR_IO)
+    {
+      // s_read_adapter_thread_running is cleared by the joiner, not the stopper.
+
+      // Reset the device, which may trigger a replug.
+      error = libusb_reset_device(s_handle);
+      ERROR_LOG_FMT(CONTROLLERINTERFACE, "Read: libusb_reset_device: {}",
+                    LibusbUtils::ErrorWrap(error));
+
+      // If error is nonzero, try fixing it next loop iteration. We can't easily return
+      // and cleanup program state without getting another thread to call Reset().
+    }
 
     ProcessInputPayload(input_buffer.data(), payload_size);
 
@@ -614,8 +625,8 @@ static bool CheckDeviceAccess(libusb_device* device)
 
 static void AddGCAdapter(libusb_device* device)
 {
-  libusb_config_descriptor* config = nullptr;
-  if (const int error = libusb_get_config_descriptor(device, 0, &config); error != LIBUSB_SUCCESS)
+  auto [error, config] = LibusbUtils::MakeConfigDescriptor(device);
+  if (error != LIBUSB_SUCCESS)
   {
     WARN_LOG_FMT(CONTROLLERINTERFACE, "libusb_get_config_descriptor failed: {}",
                  LibusbUtils::ErrorWrap(error));
@@ -636,12 +647,12 @@ static void AddGCAdapter(libusb_device* device)
       }
     }
   }
+  config.reset();
 
   int size = 0;
   std::array<u8, CONTROLER_OUTPUT_INIT_PAYLOAD_SIZE> payload = {0x13};
-  const int error =
-      libusb_interrupt_transfer(s_handle, s_endpoint_out, payload.data(),
-                                CONTROLER_OUTPUT_INIT_PAYLOAD_SIZE, &size, USB_TIMEOUT_MS);
+  error = libusb_interrupt_transfer(s_handle, s_endpoint_out, payload.data(),
+                                    CONTROLER_OUTPUT_INIT_PAYLOAD_SIZE, &size, USB_TIMEOUT_MS);
   if (error != LIBUSB_SUCCESS)
   {
     WARN_LOG_FMT(CONTROLLERINTERFACE, "AddGCAdapter: libusb_interrupt_transfer failed: {}",