diff --git a/Common/GPU/Vulkan/VulkanRenderManager.cpp b/Common/GPU/Vulkan/VulkanRenderManager.cpp
index bcde55490b..96ac910e0e 100644
--- a/Common/GPU/Vulkan/VulkanRenderManager.cpp
+++ b/Common/GPU/Vulkan/VulkanRenderManager.cpp
@@ -581,6 +581,7 @@ void VulkanRenderManager::CompileThreadFunc() {
 			}
 			toCompile = std::move(compileQueue_);
 			compileQueue_.clear();
+			compileScheduling_ = true;
 			if (!runCompileThread_) {
 				exitAfterCompile = true;
 			}
@@ -626,6 +627,11 @@ void VulkanRenderManager::CompileThreadFunc() {
 			g_threadManager.EnqueueTask(task);
 		}
 
+		{
+			std::unique_lock<std::mutex> lock(compileQueueMutex_);
+			compileScheduling_ = false;
+		}
+
 		if (exitAfterCompile) {
 			break;
 		}
@@ -904,6 +910,16 @@ void VulkanRenderManager::ReportBadStateForDraw() {
 }
 
 int VulkanRenderManager::WaitForPipelines() {
+	// Pipelines still in the queue, or taken off it but not yet made into tasks, aren't in flight yet.
+	while (true) {
+		{
+			std::unique_lock<std::mutex> lock(compileQueueMutex_);
+			if (compileQueue_.empty() && !compileScheduling_) {
+				break;
+			}
+		}
+		sleep_ms(2, "pipeline-queue-wait");
+	}
 	return CreateMultiPipelinesTask::WaitForAll();
 }
 
diff --git a/Common/GPU/Vulkan/VulkanRenderManager.h b/Common/GPU/Vulkan/VulkanRenderManager.h
index 42bb5f2dd7..0b19a4c2cb 100644
--- a/Common/GPU/Vulkan/VulkanRenderManager.h
+++ b/Common/GPU/Vulkan/VulkanRenderManager.h
@@ -628,6 +628,8 @@ private:
 	std::condition_variable compileCond_;
 	std::mutex compileQueueMutex_;
 	std::vector<CompileQueueEntry> compileQueue_;
+	// Set while the compile thread turns a batch it took off compileQueue_ into tasks.
+	bool compileScheduling_ = false;
 
 	// Thread for measuring presentation delay.
 	std::thread presentWaitThread_;