diff --git a/Source/Core/VideoBackends/D3D/D3DPerfQuery.cpp b/Source/Core/VideoBackends/D3D/D3DPerfQuery.cpp
index fe34a8ff45..f2ae05bb99 100644
--- a/Source/Core/VideoBackends/D3D/D3DPerfQuery.cpp
+++ b/Source/Core/VideoBackends/D3D/D3DPerfQuery.cpp
@@ -8,6 +8,7 @@
 #include "VideoBackends/D3D/D3DBase.h"
 #include "VideoCommon/FramebufferManager.h"
 #include "VideoCommon/VideoCommon.h"
+#include "VideoCommon/VideoConfig.h"
 
 namespace DX11
 {
@@ -96,7 +97,7 @@ u32 PerfQuery::GetQueryResult(PerfQueryType type)
     result = m_results[PQG_EFB_COPY_CLOCKS].load(std::memory_order_relaxed);
   }
 
-  return result;
+  return result / 4;
 }
 
 void PerfQuery::FlushOne()
@@ -114,8 +115,10 @@ void PerfQuery::FlushOne()
   // NOTE: Reported pixel metrics should be referenced to native resolution
   // TODO: Dropping the lower 2 bits from this count should be closer to actual
   // hardware behavior when drawing triangles.
-  const u64 native_res_result = result * EFB_WIDTH / g_framebuffer_manager->GetEFBWidth() *
-                                EFB_HEIGHT / g_framebuffer_manager->GetEFBHeight();
+  u64 native_res_result = result * EFB_WIDTH / g_framebuffer_manager->GetEFBWidth() * EFB_HEIGHT /
+                          g_framebuffer_manager->GetEFBHeight();
+  if (g_ActiveConfig.iMultisamples > 1)
+    native_res_result /= g_ActiveConfig.iMultisamples;
   m_results[entry.query_group].fetch_add(static_cast<u32>(native_res_result),
                                          std::memory_order_relaxed);
 
diff --git a/Source/Core/VideoBackends/D3D12/D3D12PerfQuery.cpp b/Source/Core/VideoBackends/D3D12/D3D12PerfQuery.cpp
index 933f118ce9..da9a6e6546 100644
--- a/Source/Core/VideoBackends/D3D12/D3D12PerfQuery.cpp
+++ b/Source/Core/VideoBackends/D3D12/D3D12PerfQuery.cpp
@@ -13,6 +13,7 @@
 #include "VideoBackends/D3D12/DX12Context.h"
 #include "VideoCommon/FramebufferManager.h"
 #include "VideoCommon/VideoCommon.h"
+#include "VideoCommon/VideoConfig.h"
 
 namespace DX12
 {
@@ -244,9 +245,11 @@ void PerfQuery::AccumulateQueriesFromBuffer(u32 query_count)
     std::memcpy(&result, mapped_ptr + (index * sizeof(PerfQueryDataType)), sizeof(result));
 
     // NOTE: Reported pixel metrics should be referenced to native resolution
-    const u64 native_res_result = static_cast<u64>(result) * EFB_WIDTH /
-                                  g_framebuffer_manager->GetEFBWidth() * EFB_HEIGHT /
-                                  g_framebuffer_manager->GetEFBHeight();
+    u64 native_res_result = static_cast<u64>(result) * EFB_WIDTH /
+                            g_framebuffer_manager->GetEFBWidth() * EFB_HEIGHT /
+                            g_framebuffer_manager->GetEFBHeight();
+    if (g_ActiveConfig.iMultisamples > 1)
+      native_res_result /= g_ActiveConfig.iMultisamples;
     m_results[entry.query_group].fetch_add(static_cast<u32>(native_res_result),
                                            std::memory_order_relaxed);
   }
diff --git a/Source/Core/VideoBackends/Metal/MTLPerfQuery.mm b/Source/Core/VideoBackends/Metal/MTLPerfQuery.mm
index 76bddc1dce..37036f28aa 100644
--- a/Source/Core/VideoBackends/Metal/MTLPerfQuery.mm
+++ b/Source/Core/VideoBackends/Metal/MTLPerfQuery.mm
@@ -46,7 +46,7 @@ u32 Metal::PerfQuery::GetQueryResult(PerfQueryType type)
     result = m_results[PQG_EFB_COPY_CLOCKS].load(std::memory_order_relaxed);
   }
 
-  return result;
+  return result / 4;
 }
 
 void Metal::PerfQuery::FlushResults()
diff --git a/Source/Core/VideoBackends/OGL/OGLPerfQuery.cpp b/Source/Core/VideoBackends/OGL/OGLPerfQuery.cpp
index 6303464251..b7e7cc0301 100644
--- a/Source/Core/VideoBackends/OGL/OGLPerfQuery.cpp
+++ b/Source/Core/VideoBackends/OGL/OGLPerfQuery.cpp
@@ -80,7 +80,7 @@ u32 PerfQuery::GetQueryResult(PerfQueryType type)
     result = m_results[PQG_EFB_COPY_CLOCKS].load(std::memory_order_relaxed);
   }
 
-  return result;
+  return result / 4;
 }
 
 // Implementations
diff --git a/Source/Core/VideoBackends/Vulkan/VKPerfQuery.cpp b/Source/Core/VideoBackends/Vulkan/VKPerfQuery.cpp
index d16c8c379b..c6aee79327 100644
--- a/Source/Core/VideoBackends/Vulkan/VKPerfQuery.cpp
+++ b/Source/Core/VideoBackends/Vulkan/VKPerfQuery.cpp
@@ -17,6 +17,7 @@
 #include "VideoBackends/Vulkan/VulkanContext.h"
 #include "VideoCommon/FramebufferManager.h"
 #include "VideoCommon/VideoCommon.h"
+#include "VideoCommon/VideoConfig.h"
 
 namespace Vulkan
 {
@@ -218,9 +219,11 @@ void PerfQuery::ReadbackQueries(u32 query_count)
     entry.has_value = false;
 
     // NOTE: Reported pixel metrics should be referenced to native resolution
-    const u64 native_res_result = static_cast<u64>(m_query_result_buffer[i]) * EFB_WIDTH /
-                                  g_framebuffer_manager->GetEFBWidth() * EFB_HEIGHT /
-                                  g_framebuffer_manager->GetEFBHeight();
+    u64 native_res_result = static_cast<u64>(m_query_result_buffer[i]) * EFB_WIDTH /
+                            g_framebuffer_manager->GetEFBWidth() * EFB_HEIGHT /
+                            g_framebuffer_manager->GetEFBHeight();
+    if (g_ActiveConfig.iMultisamples > 1)
+      native_res_result /= g_ActiveConfig.iMultisamples;
     m_results[entry.query_group].fetch_add(static_cast<u32>(native_res_result),
                                            std::memory_order_relaxed);
   }