diff --git a/Common/GPU/Vulkan/VulkanContext.cpp b/Common/GPU/Vulkan/VulkanContext.cpp
index 8e523d0bf2b7..72bdd3dca9d5 100644
--- a/Common/GPU/Vulkan/VulkanContext.cpp
+++ b/Common/GPU/Vulkan/VulkanContext.cpp
@@ -761,11 +761,6 @@ VkResult VulkanContext::CreateDevice() {
 		break;
 	}
 
-
-	for (int i = 0; i < ARRAY_SIZE(frame_); i++) {
-		frame_[i].profiler.Init(this);
-	}
-
 	return res;
 }
 
@@ -909,6 +904,10 @@ VkResult VulkanContext::ReinitSurface() {
 		return VK_ERROR_INITIALIZATION_FAILED;
 	}
 
+	for (int i = 0; i < ARRAY_SIZE(frame_); i++) {
+		frame_[i].profiler.Init(this);
+	}
+
 	return VK_SUCCESS;
 }
 
@@ -938,7 +937,7 @@ bool VulkanContext::ChooseQueue() {
 	}
 	if (presentQueueNodeIndex == UINT32_MAX) {
 		// If didn't find a queue that supports both graphics and present, then
-		// find a separate present queue.
+		// find a separate present queue. NOTE: We don't actually currently support this arrangement!
 		for (uint32_t i = 0; i < queue_count; ++i) {
 			if (supportsPresent[i] == VK_TRUE) {
 				presentQueueNodeIndex = i;
@@ -1236,13 +1235,13 @@ void VulkanContext::DestroyDevice() {
 		ERROR_LOG(G3D, "DestroyDevice: Surface should have been destroyed.");
 	}
 
-	INFO_LOG(G3D, "VulkanContext::DestroyDevice (performing deletes)");
-	PerformPendingDeletes();
-
 	for (int i = 0; i < ARRAY_SIZE(frame_); i++) {
 		frame_[i].profiler.Shutdown();
 	}
 
+	INFO_LOG(G3D, "VulkanContext::DestroyDevice (performing deletes)");
+	PerformPendingDeletes();
+
 	vmaDestroyAllocator(allocator_);
 	allocator_ = VK_NULL_HANDLE;
 
@@ -1515,6 +1514,10 @@ void VulkanDeleteList::PerformDeletes(VkDevice device, VmaAllocator allocator) {
 		vkDestroyDescriptorSetLayout(device, descSetLayout, nullptr);
 	}
 	descSetLayouts_.clear();
+	for (auto &queryPool : queryPools_) {
+		vkDestroyQueryPool(device, queryPool, nullptr);
+	}
+	queryPools_.clear();
 }
 
 void VulkanContext::GetImageMemoryRequirements(VkImage image, VkMemoryRequirements *mem_reqs, bool *dedicatedAllocation) {
diff --git a/Common/GPU/Vulkan/VulkanContext.h b/Common/GPU/Vulkan/VulkanContext.h
index 5150e908a827..072bbfa4da5c 100644
--- a/Common/GPU/Vulkan/VulkanContext.h
+++ b/Common/GPU/Vulkan/VulkanContext.h
@@ -117,6 +117,7 @@ class VulkanDeleteList {
 	void QueueDeleteFramebuffer(VkFramebuffer &framebuffer) { _dbg_assert_(framebuffer != VK_NULL_HANDLE); framebuffers_.push_back(framebuffer); framebuffer = VK_NULL_HANDLE; }
 	void QueueDeletePipelineLayout(VkPipelineLayout &pipelineLayout) { _dbg_assert_(pipelineLayout != VK_NULL_HANDLE); pipelineLayouts_.push_back(pipelineLayout); pipelineLayout = VK_NULL_HANDLE; }
 	void QueueDeleteDescriptorSetLayout(VkDescriptorSetLayout &descSetLayout) { _dbg_assert_(descSetLayout != VK_NULL_HANDLE); descSetLayouts_.push_back(descSetLayout); descSetLayout = VK_NULL_HANDLE; }
+	void QueueDeleteQueryPool(VkQueryPool &queryPool) { _dbg_assert_(queryPool != VK_NULL_HANDLE); queryPools_.push_back(queryPool); queryPool = VK_NULL_HANDLE; }
 	void QueueCallback(void(*func)(void *userdata), void *userdata) { callbacks_.push_back(Callback(func, userdata)); }
 
 	void QueueDeleteBufferAllocation(VkBuffer &buffer, VmaAllocation &alloc) { 
@@ -152,6 +153,7 @@ class VulkanDeleteList {
 	std::vector<VkFramebuffer> framebuffers_;
 	std::vector<VkPipelineLayout> pipelineLayouts_;
 	std::vector<VkDescriptorSetLayout> descSetLayouts_;
+	std::vector<VkQueryPool> queryPools_;
 	std::vector<Callback> callbacks_;
 };
 
@@ -386,10 +388,11 @@ class VulkanContext {
 	bool CheckLayers(const std::vector<LayerProperties> &layer_props, const std::vector<const char *> &layer_names) const;
 
 	WindowSystem winsys_;
+
 	// Don't use the real types here to avoid having to include platform-specific stuff
 	// that we really don't want in everything that uses VulkanContext.
-	void *winsysData1_;
-	void *winsysData2_;
+	void *winsysData1_ = nullptr;
+	void *winsysData2_ = nullptr;
 	std::function<VkExtent2D()> cbGetDrawSize_;
 
 	VkInstance instance_ = VK_NULL_HANDLE;
diff --git a/Common/GPU/Vulkan/VulkanProfiler.cpp b/Common/GPU/Vulkan/VulkanProfiler.cpp
index b073b298a1d5..a31952b1bcf0 100644
--- a/Common/GPU/Vulkan/VulkanProfiler.cpp
+++ b/Common/GPU/Vulkan/VulkanProfiler.cpp
@@ -8,7 +8,14 @@ using namespace PPSSPP_VK;
 void VulkanProfiler::Init(VulkanContext *vulkan) {
 	vulkan_ = vulkan;
 
-	validBits_ = vulkan_->GetQueueFamilyProperties(vulkan_->GetGraphicsQueueFamilyIndex()).timestampValidBits;
+	int graphicsQueueFamilyIndex = vulkan_->GetGraphicsQueueFamilyIndex();
+	_assert_(graphicsQueueFamilyIndex >= 0);
+
+	if (queryPool_) {
+		vulkan->Delete().QueueDeleteQueryPool(queryPool_);
+	}
+
+	validBits_ = vulkan_->GetQueueFamilyProperties(graphicsQueueFamilyIndex).timestampValidBits;
 
 	if (validBits_) {
 		VkQueryPoolCreateInfo ci{ VK_STRUCTURE_TYPE_QUERY_POOL_CREATE_INFO };
@@ -20,7 +27,7 @@ void VulkanProfiler::Init(VulkanContext *vulkan) {
 
 void VulkanProfiler::Shutdown() {
 	if (queryPool_) {
-		vkDestroyQueryPool(vulkan_->GetDevice(), queryPool_, nullptr);
+		vulkan_->Delete().QueueDeleteQueryPool(queryPool_);
 	}
 }