diff --git a/src/win32_window.c b/src/win32_window.c
index 0b5ccb5a..c7434f9a 100644
--- a/src/win32_window.c
+++ b/src/win32_window.c
@@ -417,10 +417,15 @@ static void updateFramebufferTransparency(const _GLFWwindow* window)
     else
     {
         LONG exStyle = GetWindowLongW(window->win32.handle, GWL_EXSTYLE);
-        exStyle &= ~WS_EX_LAYERED;
-        SetWindowLongW(window->win32.handle, GWL_EXSTYLE, exStyle);
-        RedrawWindow(window->win32.handle, NULL, NULL,
-                     RDW_ERASE | RDW_INVALIDATE | RDW_FRAME);
+        if (exStyle & WS_EX_TRANSPARENT)
+            SetLayeredWindowAttributes(window->win32.handle, 0, 0, 0);
+        else
+        {
+            exStyle &= ~WS_EX_LAYERED;
+            SetWindowLongW(window->win32.handle, GWL_EXSTYLE, exStyle);
+            RedrawWindow(window->win32.handle, NULL, NULL,
+                         RDW_ERASE | RDW_INVALIDATE | RDW_FRAME);
+        }
     }
 }
 
@@ -1201,13 +1206,6 @@ static LRESULT CALLBACK windowProc(HWND hWnd, UINT uMsg,
             DragFinish(drop);
             return 0;
         }
-
-        case WM_NCHITTEST:
-        {
-            if (window->mousePassthrough)
-                return HTTRANSPARENT;
-            break;
-        }
     }
 
     return DefWindowProcW(hWnd, uMsg, wParam, lParam);
@@ -1863,6 +1861,33 @@ void _glfwPlatformSetWindowFloating(_GLFWwindow* window, GLFWbool enabled)
 
 void _glfwPlatformSetWindowMousePassthrough(_GLFWwindow* window, GLFWbool enabled)
 {
+    COLORREF key = 0;
+    BYTE alpha = 0;
+    DWORD flags = 0;
+    DWORD exStyle = GetWindowLongW(window->win32.handle, GWL_EXSTYLE);
+
+    if (exStyle & WS_EX_LAYERED)
+        GetLayeredWindowAttributes(window->win32.handle, &key, &alpha, &flags);
+
+    if (enabled)
+        exStyle |= (WS_EX_TRANSPARENT | WS_EX_LAYERED);
+    else
+    {
+        exStyle &= ~WS_EX_TRANSPARENT;
+        // NOTE: Window opacity and framebuffer transparency also need to
+        //       control the layered style so avoid stepping on their feet
+        if (exStyle & WS_EX_LAYERED)
+        {
+            if (!(flags & (LWA_ALPHA | LWA_COLORKEY)))
+                exStyle &= ~WS_EX_LAYERED;
+        }
+    }
+
+    SetWindowLongW(window->win32.handle, GWL_EXSTYLE, exStyle);
+
+    if (enabled)
+        SetLayeredWindowAttributes(window->win32.handle, key, alpha, flags);
+
     window->mousePassthrough = enabled;
 }
 
@@ -1883,19 +1908,22 @@ float _glfwPlatformGetWindowOpacity(_GLFWwindow* window)
 
 void _glfwPlatformSetWindowOpacity(_GLFWwindow* window, float opacity)
 {
-    if (opacity < 1.f)
+    LONG exStyle = GetWindowLongW(window->win32.handle, GWL_EXSTYLE);
+    if (opacity < 1.f || (exStyle & WS_EX_TRANSPARENT))
     {
         const BYTE alpha = (BYTE) (255 * opacity);
-        DWORD style = GetWindowLongW(window->win32.handle, GWL_EXSTYLE);
-        style |= WS_EX_LAYERED;
-        SetWindowLongW(window->win32.handle, GWL_EXSTYLE, style);
+        exStyle |= WS_EX_LAYERED;
+        SetWindowLongW(window->win32.handle, GWL_EXSTYLE, exStyle);
         SetLayeredWindowAttributes(window->win32.handle, 0, alpha, LWA_ALPHA);
     }
+    else if (exStyle & WS_EX_TRANSPARENT)
+    {
+        SetLayeredWindowAttributes(window->win32.handle, 0, 0, 0);
+    }
     else
     {
-        DWORD style = GetWindowLongW(window->win32.handle, GWL_EXSTYLE);
-        style &= ~WS_EX_LAYERED;
-        SetWindowLongW(window->win32.handle, GWL_EXSTYLE, style);
+        exStyle &= ~WS_EX_LAYERED;
+        SetWindowLongW(window->win32.handle, GWL_EXSTYLE, exStyle);
     }
 }