diff --git a/Ryujinx.Graphics.Vulkan/PipelineFull.cs b/Ryujinx.Graphics.Vulkan/PipelineFull.cs
index 0d461b213..e25f8bdf0 100644
--- a/Ryujinx.Graphics.Vulkan/PipelineFull.cs
+++ b/Ryujinx.Graphics.Vulkan/PipelineFull.cs
@@ -206,16 +206,25 @@ namespace Ryujinx.Graphics.Vulkan
 
             // The GPU will flush the queries to CPU and evaluate the condition there instead.
 
-            FlushCommandsImpl(); // The thread will be stalled manually flushing the counter, so flush GL commands now.
+            FlushPendingQuery(); // The thread will be stalled manually flushing the counter, so flush commands now.
             return false;
         }
 
         public bool TryHostConditionalRendering(ICounterEvent value, ICounterEvent compare, bool isEqual)
         {
-            FlushCommandsImpl(); // The thread will be stalled manually flushing the counter, so flush GL commands now.
+            FlushPendingQuery(); // The thread will be stalled manually flushing the counter, so flush commands now.
             return false;
         }
 
+        private void FlushPendingQuery()
+        {
+            if (_hasPendingQuery)
+            {
+                _hasPendingQuery = false;
+                FlushCommandsImpl();
+            }
+        }
+
         public void FlushCommandsImpl([System.Runtime.CompilerServices.CallerMemberName] string caller = "")
         {
             // System.Console.WriteLine("flush by " + caller);
@@ -285,11 +294,7 @@ namespace Ryujinx.Graphics.Vulkan
 
         protected override void SignalProgramChange()
         {
-            if (_hasPendingQuery)
-            {
-                _hasPendingQuery = false;
-                FlushCommandsImpl();
-            }
+            FlushPendingQuery();
         }
     }
 }
diff --git a/Ryujinx.Graphics.Vulkan/Queries/CounterQueue.cs b/Ryujinx.Graphics.Vulkan/Queries/CounterQueue.cs
index 197cd5b5c..6f0b25c60 100644
--- a/Ryujinx.Graphics.Vulkan/Queries/CounterQueue.cs
+++ b/Ryujinx.Graphics.Vulkan/Queries/CounterQueue.cs
@@ -21,12 +21,14 @@ namespace Ryujinx.Graphics.Vulkan.Queries
         private CounterQueueEvent _current;
 
         private ulong _accumulatedCounter;
+        private int _waiterCount;
 
         private object _lock = new object();
 
         private Queue<BufferedQuery> _queryPool;
         private AutoResetEvent _queuedEvent = new AutoResetEvent(false);
         private AutoResetEvent _wakeSignal = new AutoResetEvent(false);
+        private AutoResetEvent _eventConsumed = new AutoResetEvent(false);
 
         private Thread _consumerThread;
 
@@ -69,7 +71,13 @@ namespace Ryujinx.Graphics.Vulkan.Queries
                 }
                 else
                 {
-                    evt.TryConsume(ref _accumulatedCounter, true, _wakeSignal);
+                    // Spin-wait rather than sleeping if there are any waiters, by passing null instead of the wake signal.
+                    evt.TryConsume(ref _accumulatedCounter, true, _waiterCount == 0 ? _wakeSignal : null);
+                }
+
+                if (_waiterCount > 0)
+                {
+                    _eventConsumed.Set();
                 }
             }
         }
@@ -175,32 +183,17 @@ namespace Ryujinx.Graphics.Vulkan.Queries
 
         public void FlushTo(CounterQueueEvent evt)
         {
-            lock (_lock)
+            // Flush the counter queue on the main thread.
+            Interlocked.Increment(ref _waiterCount);
+
+            _wakeSignal.Set();
+
+            while (!evt.Disposed)
             {
-                if (evt.Disposed)
-                {
-                    return;
-                }
-
-                // Tell the queue to process all events up to this one.
-                while (_events.Count > 0)
-                {
-                    CounterQueueEvent flush = _events.Peek();
-
-                    if (flush.DrawIndex > evt.DrawIndex)
-                    {
-                        return;
-                    }
-
-                    _events.Dequeue();
-                    flush.TryConsume(ref _accumulatedCounter, true);
-
-                    if (flush == evt)
-                    {
-                        return;
-                    }
-                }
+                _eventConsumed.WaitOne(1);
             }
+
+            Interlocked.Decrement(ref _waiterCount);
         }
 
         public void Dispose()
@@ -227,6 +220,10 @@ namespace Ryujinx.Graphics.Vulkan.Queries
             {
                 query.Dispose();
             }
+
+            _queuedEvent.Dispose();
+            _wakeSignal.Dispose();
+            _eventConsumed.Dispose();
         }
     }
 }