diff --git a/Common/GPU/Vulkan/VulkanFrameData.cpp b/Common/GPU/Vulkan/VulkanFrameData.cpp
index e8d6f67784..d5bc6f47aa 100644
--- a/Common/GPU/Vulkan/VulkanFrameData.cpp
+++ b/Common/GPU/Vulkan/VulkanFrameData.cpp
@@ -1,3 +1,5 @@
+#include <mutex>
+
 #include "VulkanFrameData.h"
 #include "Common/Log.h"
 
@@ -26,6 +28,7 @@ void FrameData::Init(VulkanContext *vulkan, int index) {
 
 	// Creating the frame fence with true so they can be instantly waited on the first frame
 	fence = vulkan->CreateFence(true);
+	readyForFence = true;
 
 	// This fence one is used for synchronizing readbacks. Does not need preinitialization.
 	readbackFence = vulkan->CreateFence(false);
@@ -169,7 +172,18 @@ void FrameData::SubmitPending(VulkanContext *vulkan, FrameSubmitType type, Frame
 		submit_info.signalSemaphoreCount = 1;
 		submit_info.pSignalSemaphores = &sharedData.renderingCompleteSemaphore;
 	}
-	VkResult res = vkQueueSubmit(vulkan->GetGraphicsQueue(), 1, &submit_info, fenceToTrigger);
+
+	VkResult res;
+	if (fenceToTrigger == fence) {
+		// The fence is waited on by the main thread, they are not allowed to access it simultaneously.
+		std::lock_guard<std::mutex> lock(fenceMutex);
+		res = vkQueueSubmit(vulkan->GetGraphicsQueue(), 1, &submit_info, fenceToTrigger);
+		readyForFence = true;
+		fenceCondVar.notify_one();
+	} else {
+		res = vkQueueSubmit(vulkan->GetGraphicsQueue(), 1, &submit_info, fenceToTrigger);
+	}
+
 	if (res == VK_ERROR_DEVICE_LOST) {
 		_assert_msg_(false, "Lost the Vulkan device in vkQueueSubmit! If this happens again, switch Graphics Backend away from Vulkan");
 	} else {
diff --git a/Common/GPU/Vulkan/VulkanFrameData.h b/Common/GPU/Vulkan/VulkanFrameData.h
index a80210e81c..9fdd865ebf 100644
--- a/Common/GPU/Vulkan/VulkanFrameData.h
+++ b/Common/GPU/Vulkan/VulkanFrameData.h
@@ -44,6 +44,10 @@ enum class FrameSubmitType {
 struct FrameData {
 	bool skipSwap = false;
 
+	std::mutex fenceMutex;
+	std::condition_variable fenceCondVar;
+	bool readyForFence = true;
+
 	VkFence fence;
 	VkFence readbackFence;  // Strictly speaking we might only need one global of these.
 
diff --git a/Common/GPU/Vulkan/VulkanRenderManager.cpp b/Common/GPU/Vulkan/VulkanRenderManager.cpp
index 4229ed5d86..c307314233 100644
--- a/Common/GPU/Vulkan/VulkanRenderManager.cpp
+++ b/Common/GPU/Vulkan/VulkanRenderManager.cpp
@@ -504,6 +504,16 @@ void VulkanRenderManager::BeginFrame(bool enableProfiling, bool enableLogProfile
 
 	VLOG("PUSH: Fencing %d", curFrame);
 
+	// Makes sure the submission from the previous time around has happened. Otherwise
+	// we are not allowed to wait from another thread here..
+	{
+		std::unique_lock<std::mutex> lock(frameData.fenceMutex);
+		while (!frameData.readyForFence) {
+			frameData.fenceCondVar.wait(lock);
+		}
+		frameData.readyForFence = false;
+	}
+
 	// This must be the very first Vulkan call we do in a new frame.
 	// Makes sure the very last command buffer from the frame before the previous has been fully executed.
 	if (vkWaitForFences(device, 1, &frameData.fence, true, UINT64_MAX) == VK_ERROR_DEVICE_LOST) {