diff --git a/Source/Core/VideoBackends/OGL/OGLRender.cpp b/Source/Core/VideoBackends/OGL/OGLRender.cpp
index d3435c51d5..bf0650f961 100644
--- a/Source/Core/VideoBackends/OGL/OGLRender.cpp
+++ b/Source/Core/VideoBackends/OGL/OGLRender.cpp
@@ -856,30 +856,12 @@ void Renderer::SetScissorRect(const MathUtil::Rectangle<int>& rc)
 
 u16 Renderer::BBoxReadImpl(int index)
 {
-  // swap 2 and 3 for top/bottom
-  if (index >= 2)
-    index ^= 1;
-
-  int value = BoundingBox::Get(index);
-  if (index >= 2)
-  {
-    // up/down -- we have to swap up and down
-    value = EFB_HEIGHT - value;
-  }
-
-  return static_cast<u16>(value);
+  return static_cast<u16>(BoundingBox::Get(index));
 }
 
 void Renderer::BBoxWriteImpl(int index, u16 value)
 {
-  s32 swapped_value = value;
-  if (index >= 2)
-  {
-    index ^= 1;  // swap 2 and 3 for top/bottom
-    swapped_value = EFB_HEIGHT - swapped_value;
-  }
-
-  BoundingBox::Set(index, swapped_value);
+  BoundingBox::Set(index, value);
 }
 
 void Renderer::BBoxFlushImpl()
diff --git a/Source/Core/VideoCommon/PixelShaderGen.cpp b/Source/Core/VideoCommon/PixelShaderGen.cpp
index 80d6c09573..37e856ae42 100644
--- a/Source/Core/VideoCommon/PixelShaderGen.cpp
+++ b/Source/Core/VideoCommon/PixelShaderGen.cpp
@@ -499,16 +499,15 @@ void UpdateBoundingBox(float2 rawpos) {{
   // such that width = right - left + 1. This has been verified on hardware.
   int2 pos = int2(rawpos * cefbscale);
 
+#ifdef API_OPENGL
+  // We need to invert the Y coordinate due to OpenGL's lower-left origin
+  pos.y = {efb_height} - pos.y - 1;
+#endif
+
   // The GC/Wii GPU rasterizes in 2x2 pixel groups, so bounding box values will be rounded to the
   // extents of these groups, rather than the exact pixel.
-#ifdef API_OPENGL
-  // Need to flip the operands for Y on OpenGL because of lower-left origin.
-  int2 pos_tl = int2(pos.x & ~1, pos.y | 1);
-  int2 pos_br = int2(pos.x | 1, pos.y & ~1);
-#else
   int2 pos_tl = pos & ~1;
   int2 pos_br = pos | 1;
-#endif
 
 #ifdef SUPPORTS_SUBGROUP_REDUCTION
   if (CAN_USE_SUBGROUP_REDUCTION) {{
@@ -526,7 +525,8 @@ void UpdateBoundingBox(float2 rawpos) {{
 #endif
 }}
 
-)");
+)",
+              fmt::arg("efb_height", EFB_HEIGHT));
   }
 }