diff --git a/Source/Core/Core/HW/WiimoteReal/WiimoteReal.cpp b/Source/Core/Core/HW/WiimoteReal/WiimoteReal.cpp
index ad310852f0..cbcefc7aab 100644
--- a/Source/Core/Core/HW/WiimoteReal/WiimoteReal.cpp
+++ b/Source/Core/Core/HW/WiimoteReal/WiimoteReal.cpp
@@ -708,15 +708,19 @@ void WiimoteScanner::ThreadFunc()
       g_controller_interface.PlatformPopulateDevices([] { ProcessWiimotePool(); });
     }
 
+    if (m_scan_mode.load() == WiimoteScanMode::DO_NOT_SCAN)
+      continue;
+
+    // Stop scanning if not in continous mode.
+    auto scan_mode = WiimoteScanMode::SCAN_ONCE;
+    m_scan_mode.compare_exchange_strong(scan_mode, WiimoteScanMode::DO_NOT_SCAN);
+
     // Does stuff needed to detect disconnects on Windows
     for (const auto& backend : m_backends)
       backend->Update();
 
     CheckForDisconnectedWiimotes();
 
-    if (m_scan_mode.load() == WiimoteScanMode::DO_NOT_SCAN)
-      continue;
-
     // If we don't want Wiimotes in ControllerInterface, we may not need them at all.
     if (!Config::Get(Config::MAIN_CONNECT_WIIMOTES_FOR_CONTROLLER_INTERFACE))
     {
@@ -761,10 +765,6 @@ void WiimoteScanner::ThreadFunc()
         }
       }
     }
-
-    // Stop scanning if not in continous mode.
-    auto scan_mode = WiimoteScanMode::SCAN_ONCE;
-    m_scan_mode.compare_exchange_strong(scan_mode, WiimoteScanMode::DO_NOT_SCAN);
   }
 
   {