diff --git a/Ryujinx.Graphics.Vulkan/AutoFlushCounter.cs b/Ryujinx.Graphics.Vulkan/AutoFlushCounter.cs
index 4ba689ccb4..2a4cbd52e6 100644
--- a/Ryujinx.Graphics.Vulkan/AutoFlushCounter.cs
+++ b/Ryujinx.Graphics.Vulkan/AutoFlushCounter.cs
@@ -1,5 +1,6 @@
 using System;
 using System.Diagnostics;
+using System.Linq;
 
 namespace Ryujinx.Graphics.Vulkan
 {
@@ -16,6 +17,10 @@ namespace Ryujinx.Graphics.Vulkan
         private bool _hasPendingQuery;
         private int _queryCount;
 
+        private int[] _queryCountHistory = new int[3];
+        private int _queryCountHistoryIndex;
+        private int _remainingQueries;
+
         public void RegisterFlush(ulong drawCount)
         {
             _lastFlush = Stopwatch.GetTimestamp();
@@ -27,6 +32,9 @@ namespace Ryujinx.Graphics.Vulkan
         public bool RegisterPendingQuery()
         {
             _hasPendingQuery = true;
+            _remainingQueries--;
+
+            _queryCountHistory[_queryCountHistoryIndex]++;
 
             // Interrupt render passes to flush queries, so that early results arrive sooner.
             if (++_queryCount == InitialQueryCountForFlush)
@@ -37,6 +45,21 @@ namespace Ryujinx.Graphics.Vulkan
             return false;
         }
 
+        public int GetRemainingQueries()
+        {
+            if (_remainingQueries <= 0)
+            {
+                _remainingQueries = 16;
+            }
+
+            if (_queryCount < InitialQueryCountForFlush)
+            {
+                return Math.Min(InitialQueryCountForFlush - _queryCount, _remainingQueries);
+            }
+
+            return _remainingQueries;
+        }
+
         public bool ShouldFlushQuery()
         {
             return _hasPendingQuery;
@@ -69,5 +92,14 @@ namespace Ryujinx.Graphics.Vulkan
 
             return now > _lastFlush + flushTimeout;
         }
+
+        public void Present()
+        {
+            _queryCountHistoryIndex = (_queryCountHistoryIndex + 1) % 3;
+
+            _remainingQueries = _queryCountHistory.Max() + 10;
+
+            _queryCountHistory[_queryCountHistoryIndex] = 0;
+        }
     }
 }
diff --git a/Ryujinx.Graphics.Vulkan/PipelineBase.cs b/Ryujinx.Graphics.Vulkan/PipelineBase.cs
index 1c0c836bba..c53acfe104 100644
--- a/Ryujinx.Graphics.Vulkan/PipelineBase.cs
+++ b/Ryujinx.Graphics.Vulkan/PipelineBase.cs
@@ -22,7 +22,7 @@ namespace Ryujinx.Graphics.Vulkan
         protected readonly Device Device;
         public readonly PipelineCache PipelineCache;
 
-        protected readonly AutoFlushCounter AutoFlush;
+        public readonly AutoFlushCounter AutoFlush;
 
         protected PipelineDynamicState DynamicState;
         private PipelineState _newState;
diff --git a/Ryujinx.Graphics.Vulkan/PipelineFull.cs b/Ryujinx.Graphics.Vulkan/PipelineFull.cs
index 5b4f4a6e9f..94fd24416d 100644
--- a/Ryujinx.Graphics.Vulkan/PipelineFull.cs
+++ b/Ryujinx.Graphics.Vulkan/PipelineFull.cs
@@ -14,7 +14,6 @@ namespace Ryujinx.Graphics.Vulkan
         private CounterQueueEvent _activeConditionalRender;
 
         private readonly List<BufferedQuery> _pendingQueryCopies;
-        private readonly List<BufferedQuery> _pendingQueryResets;
 
         private ulong _byteWeight;
 
@@ -22,7 +21,6 @@ namespace Ryujinx.Graphics.Vulkan
         {
             _activeQueries = new List<QueryPool>();
             _pendingQueryCopies = new();
-            _pendingQueryResets = new List<BufferedQuery>();
 
             CommandBuffer = (Cbs = gd.CommandBufferPool.Rent()).CommandBuffer;
         }
@@ -34,16 +32,6 @@ namespace Ryujinx.Graphics.Vulkan
                 query.PoolCopy(Cbs);
             }
 
-            lock (_pendingQueryResets)
-            {
-                foreach (var query in _pendingQueryResets)
-                {
-                    query.PoolReset(CommandBuffer);
-                }
-
-                _pendingQueryResets.Clear();
-            }
-
             _pendingQueryCopies.Clear();
         }
 
@@ -238,10 +226,12 @@ namespace Ryujinx.Graphics.Vulkan
                 Gd.Api.CmdBeginQuery(CommandBuffer, queryPool, 0, Gd.Capabilities.SupportsPreciseOcclusionQueries ? QueryControlFlags.PreciseBit : 0);
             }
 
+            Gd.ResetCounterPool();
+
             Restore();
         }
 
-        public void BeginQuery(BufferedQuery query, QueryPool pool, bool needsReset)
+        public void BeginQuery(BufferedQuery query, QueryPool pool, bool needsReset, bool fromSamplePool)
         {
             if (needsReset)
             {
@@ -249,9 +239,11 @@ namespace Ryujinx.Graphics.Vulkan
 
                 Gd.Api.CmdResetQueryPool(CommandBuffer, pool, 0, 1);
 
-                lock (_pendingQueryResets)
+                if (fromSamplePool)
                 {
-                    _pendingQueryResets.Remove(query); // Might be present on here.
+                    // Try reset some additional queries in advance.
+
+                    Gd.ResetFutureCounters(CommandBuffer, AutoFlush.GetRemainingQueries());
                 }
             }
 
@@ -267,14 +259,6 @@ namespace Ryujinx.Graphics.Vulkan
             _activeQueries.Remove(pool);
         }
 
-        public void ResetQuery(BufferedQuery query)
-        {
-            lock (_pendingQueryResets)
-            {
-                _pendingQueryResets.Add(query);
-            }
-        }
-
         public void CopyQueryResults(BufferedQuery query)
         {
             _pendingQueryCopies.Add(query);
diff --git a/Ryujinx.Graphics.Vulkan/Queries/BufferedQuery.cs b/Ryujinx.Graphics.Vulkan/Queries/BufferedQuery.cs
index 4cf258eb78..a1a5eb2794 100644
--- a/Ryujinx.Graphics.Vulkan/Queries/BufferedQuery.cs
+++ b/Ryujinx.Graphics.Vulkan/Queries/BufferedQuery.cs
@@ -18,7 +18,6 @@ namespace Ryujinx.Graphics.Vulkan.Queries
         private readonly PipelineFull _pipeline;
 
         private QueryPool _queryPool;
-        private bool _isReset;
 
         private readonly BufferHolder _buffer;
         private readonly IntPtr _bufferMap;
@@ -27,6 +26,7 @@ namespace Ryujinx.Graphics.Vulkan.Queries
         private bool _isSupported;
 
         private long _defaultValue;
+        private int? _resetSequence;
 
         public unsafe BufferedQuery(VulkanRenderer gd, Device device, PipelineFull pipeline, CounterType type, bool result32Bit)
         {
@@ -92,16 +92,17 @@ namespace Ryujinx.Graphics.Vulkan.Queries
         public void Reset()
         {
             End(false);
-            Begin();
+            Begin(null);
         }
 
-        public void Begin()
+        public void Begin(int? resetSequence)
         {
             if (_isSupported)
             {
-                _pipeline.BeginQuery(this, _queryPool, !_isReset);
+                bool needsReset = resetSequence == null || _resetSequence == null || resetSequence.Value != _resetSequence.Value;
+                _pipeline.BeginQuery(this, _queryPool, needsReset, _type == CounterType.SamplesPassed && resetSequence != null);
             }
-            _isReset = false;
+            _resetSequence = null;
         }
 
         public unsafe void End(bool withResult)
@@ -162,13 +163,14 @@ namespace Ryujinx.Graphics.Vulkan.Queries
             return data;
         }
 
-        public void PoolReset(CommandBuffer cmd)
+        public void PoolReset(CommandBuffer cmd, int resetSequence)
         {
             if (_isSupported)
             {
                 _api.CmdResetQueryPool(cmd, _queryPool, 0, 1);
             }
-            _isReset = true;
+
+            _resetSequence = resetSequence;
         }
 
         public void PoolCopy(CommandBufferScoped cbs)
diff --git a/Ryujinx.Graphics.Vulkan/Queries/CounterQueue.cs b/Ryujinx.Graphics.Vulkan/Queries/CounterQueue.cs
index 7ee3c15aec..c47f95eab8 100644
--- a/Ryujinx.Graphics.Vulkan/Queries/CounterQueue.cs
+++ b/Ryujinx.Graphics.Vulkan/Queries/CounterQueue.cs
@@ -3,6 +3,7 @@ using Silk.NET.Vulkan;
 using System;
 using System.Collections.Generic;
 using System.Threading;
+using System.Linq;
 
 namespace Ryujinx.Graphics.Vulkan.Queries
 {
@@ -32,6 +33,8 @@ namespace Ryujinx.Graphics.Vulkan.Queries
 
         private Thread _consumerThread;
 
+        public int ResetSequence { get; private set; }
+
         internal CounterQueue(VulkanRenderer gd, Device device, PipelineFull pipeline, CounterType type)
         {
             _gd = gd;
@@ -53,6 +56,24 @@ namespace Ryujinx.Graphics.Vulkan.Queries
             _consumerThread.Start();
         }
 
+        public void ResetCounterPool()
+        {
+            ResetSequence++;
+        }
+
+        public void ResetFutureCounters(CommandBuffer cmd, int count)
+        {
+            // Pre-emptively reset queries to avoid render pass splitting.
+            lock (_queryPool)
+            {
+                count = Math.Min(count, _queryPool.Count);
+                for (int i = 0; i < count; i++)
+                {
+                    _queryPool.ElementAt(i).PoolReset(cmd, ResetSequence);
+                }
+            }
+        }
+
         private void EventConsumer()
         {
             while (!Disposed)
@@ -106,7 +127,7 @@ namespace Ryujinx.Graphics.Vulkan.Queries
         {
             lock (_lock)
             {
-                _pipeline.ResetQuery(query);
+                // The query will be reset when it dequeues.
                 _queryPool.Enqueue(query);
             }
         }
diff --git a/Ryujinx.Graphics.Vulkan/Queries/CounterQueueEvent.cs b/Ryujinx.Graphics.Vulkan/Queries/CounterQueueEvent.cs
index 241fe1ee08..6b780ba34a 100644
--- a/Ryujinx.Graphics.Vulkan/Queries/CounterQueueEvent.cs
+++ b/Ryujinx.Graphics.Vulkan/Queries/CounterQueueEvent.cs
@@ -34,7 +34,7 @@ namespace Ryujinx.Graphics.Vulkan.Queries
 
             DrawIndex = drawIndex;
 
-            _counter.Begin();
+            _counter.Begin(_queue.ResetSequence);
         }
 
         public Auto<DisposableBuffer> GetBuffer()
diff --git a/Ryujinx.Graphics.Vulkan/Queries/Counters.cs b/Ryujinx.Graphics.Vulkan/Queries/Counters.cs
index 63581e4271..7113d0601a 100644
--- a/Ryujinx.Graphics.Vulkan/Queries/Counters.cs
+++ b/Ryujinx.Graphics.Vulkan/Queries/Counters.cs
@@ -24,6 +24,19 @@ namespace Ryujinx.Graphics.Vulkan.Queries
             }
         }
 
+        public void ResetCounterPool()
+        {
+            foreach (var queue in _counterQueues)
+            {
+                queue.ResetCounterPool();
+            }
+        }
+
+        public void ResetFutureCounters(CommandBuffer cmd, int count)
+        {
+            _counterQueues[(int)CounterType.SamplesPassed].ResetFutureCounters(cmd, count);
+        }
+
         public CounterQueueEvent QueueReport(CounterType type, EventHandler<ulong> resultHandler, bool hostReserved)
         {
             return _counterQueues[(int)type].QueueReport(resultHandler, _pipeline.DrawCount, hostReserved);
diff --git a/Ryujinx.Graphics.Vulkan/VulkanRenderer.cs b/Ryujinx.Graphics.Vulkan/VulkanRenderer.cs
index bec7b84755..f53f794009 100644
--- a/Ryujinx.Graphics.Vulkan/VulkanRenderer.cs
+++ b/Ryujinx.Graphics.Vulkan/VulkanRenderer.cs
@@ -679,6 +679,16 @@ namespace Ryujinx.Graphics.Vulkan
             _counters.Update();
         }
 
+        public void ResetCounterPool()
+        {
+            _counters.ResetCounterPool();
+        }
+
+        public void ResetFutureCounters(CommandBuffer cmd, int count)
+        {
+            _counters?.ResetFutureCounters(cmd, count);
+        }
+
         public void BackgroundContextAction(Action action, bool alwaysBackground = false)
         {
             action();
diff --git a/Ryujinx.Graphics.Vulkan/Window.cs b/Ryujinx.Graphics.Vulkan/Window.cs
index edc7d7160d..7412ad90d9 100644
--- a/Ryujinx.Graphics.Vulkan/Window.cs
+++ b/Ryujinx.Graphics.Vulkan/Window.cs
@@ -225,6 +225,8 @@ namespace Ryujinx.Graphics.Vulkan
 
         public unsafe override void Present(ITexture texture, ImageCrop crop, Action swapBuffersCallback)
         {
+            _gd.PipelineInternal.AutoFlush.Present();
+
             uint nextImage = 0;
 
             while (true)