diff --git a/Common/GPU/GraphicsContext.h b/Common/GPU/GraphicsContext.h
index a4b2667a41..ca05a20a17 100644
--- a/Common/GPU/GraphicsContext.h
+++ b/Common/GPU/GraphicsContext.h
@@ -54,6 +54,10 @@ public:
 	// Called from the emu thread, so be ready for that.
 	virtual void NotifyEmuThreadExit() {}
 
+	// The API context that queued-up commands were recorded against is gone (or isn't current on the
+	// thread about to drain them), so they must not be executed for real. Only meaningful on Android GL.
+	virtual void NotifyContextLost() {}
+
 	// Useful for checks that need to be performed every frame.
 	// Should strive to get rid of these.
 	virtual void Poll() {}
diff --git a/Common/GPU/OpenGL/GLRenderManager.h b/Common/GPU/OpenGL/GLRenderManager.h
index edfe69b373..9c9f13f70a 100644
--- a/Common/GPU/OpenGL/GLRenderManager.h
+++ b/Common/GPU/OpenGL/GLRenderManager.h
@@ -1,5 +1,6 @@
 #pragma once
 
+#include <atomic>
 #include <thread>
 #include <unordered_map>
 #include <vector>
@@ -930,7 +931,8 @@ private:
 	bool syncDone_ = false;
 
 	GLDeleter deleter_;
-	bool skipGLCalls_ = false;
+	// Set from either thread, read on the render thread.
+	std::atomic<bool> skipGLCalls_{false};
 
 	int curFrame_ = 0;
 
diff --git a/Common/GPU/OpenGL/OpenGLGraphicsContext.h b/Common/GPU/OpenGL/OpenGLGraphicsContext.h
index 88ba27f5f3..082ac4a819 100644
--- a/Common/GPU/OpenGL/OpenGLGraphicsContext.h
+++ b/Common/GPU/OpenGL/OpenGLGraphicsContext.h
@@ -33,6 +33,12 @@ public:
 		renderManager_->ThreadEnd();
 	}
 
+	void NotifyContextLost() override {
+		if (renderManager_) {
+			renderManager_->SetSkipGLCalls();
+		}
+	}
+
 	// Call from emu thread
 	void NotifyEmuThreadExit() override {
 		renderManager_->SetSkipGLCalls();
diff --git a/android/jni/app-android.cpp b/android/jni/app-android.cpp
index 50cb99e2b2..65522d3bd6 100644
--- a/android/jni/app-android.cpp
+++ b/android/jni/app-android.cpp
@@ -899,6 +899,8 @@ extern "C" void Java_org_ppsspp_ppsspp_NativeApp_shutdown(JNIEnv *, jclass) {
 
 	if (renderer_inited && graphicsContext && graphicsContext->NeedsSeparateEmuThread()) {
 		// Only used in Java EGL path.
+		// The join drains the render queue right here, on a thread without a GL context.
+		graphicsContext->NotifyContextLost();
 		INFO_LOG(Log::System, "Joining emuthread.");
 		EmuThread_Join(graphicsContext, g_emuThread);
 
@@ -967,6 +969,9 @@ extern "C" jboolean Java_org_ppsspp_ppsspp_NativeRenderer_displayInit(JNIEnv * e
 		// but the only mechanism for handling lost devices seems to be that onSurfaceCreated is called again,
 		// which ends up calling displayInit.
 		INFO_LOG(Log::G3D, "NativeApp.displayInit(): Second time, joining the emuthread and starting it up again.");
+		// We only get here with a fresh EGL context. What's left in the render queue refers to objects
+		// from the old one, so it mustn't be run against this one when the join drains it.
+		graphicsContext->NotifyContextLost();
 		EmuThread_Join(graphicsContext, g_emuThread);
 
 		graphicsContext->ShutdownSurface();