diff --git a/Source/Core/VideoCommon/VertexManagerBase.cpp b/Source/Core/VideoCommon/VertexManagerBase.cpp
index 7987887b86..64246df904 100644
--- a/Source/Core/VideoCommon/VertexManagerBase.cpp
+++ b/Source/Core/VideoCommon/VertexManagerBase.cpp
@@ -644,9 +644,6 @@ void VertexManagerBase::Flush()
     // Same with GPU texture decoding, which uses compute shaders.
     g_texture_cache->BindTextures(used_textures, samplers);
 
-    if (PerfQueryBase::ShouldEmulate())
-      g_perf_query->EnableQuery(bpmem.zcontrol.early_ztest ? PQG_ZCOMP_ZCOMPLOC : PQG_ZCOMP);
-
     if (!skip)
     {
       UpdatePipelineConfig();
@@ -668,15 +665,9 @@ void VertexManagerBase::Flush()
       }
     }
 
-    // Track the total emulated state draws
-    INCSTAT(g_stats.this_frame.num_draw_calls);
-
     // Even if we skip the draw, emulated state should still be impacted
     OnDraw();
 
-    if (PerfQueryBase::ShouldEmulate())
-      g_perf_query->DisableQuery(bpmem.zcontrol.early_ztest ? PQG_ZCOMP_ZCOMPLOC : PQG_ZCOMP);
-
     // The EFB cache is now potentially stale.
     g_framebuffer_manager->FlagPeekCacheAsOutOfDate();
   }
@@ -1098,7 +1089,16 @@ void VertexManagerBase::RenderDrawCall(
     base_vertex <<= 2;
   }
 
+  if (PerfQueryBase::ShouldEmulate())
+    g_perf_query->EnableQuery(bpmem.zcontrol.early_ztest ? PQG_ZCOMP_ZCOMPLOC : PQG_ZCOMP);
+
   DrawCurrentBatch(base_index, m_index_generator.GetIndexLen(), base_vertex);
+
+  // Track the total emulated state draws
+  INCSTAT(g_stats.this_frame.num_draw_calls);
+
+  if (PerfQueryBase::ShouldEmulate())
+    g_perf_query->DisableQuery(bpmem.zcontrol.early_ztest ? PQG_ZCOMP_ZCOMPLOC : PQG_ZCOMP);
 }
 
 const AbstractPipeline* VertexManagerBase::GetCustomPipeline(