diff --git a/examples/demo-app/demo_app.cpp b/examples/demo-app/demo_app.cpp
index abc5ec92..f7a0d6cb 100644
--- a/examples/demo-app/demo_app.cpp
+++ b/examples/demo-app/demo_app.cpp
@@ -880,6 +880,7 @@ int main(int argc, char** argv) {
   // }
 
   std::cout << "!!!! shutdown time" << std::endl;
+  polyscope::shutdown();
 
   return 0;
 }
diff --git a/include/polyscope/messages.h b/include/polyscope/messages.h
index 01aac9ca..4e64b3a5 100644
--- a/include/polyscope/messages.h
+++ b/include/polyscope/messages.h
@@ -27,4 +27,5 @@ void exception(std::string message);
 
 // Process any warnings that have accumulated, showing them to the user and clearing the queue.
 void showDelayedWarnings();
+void clearMessages();
 } // namespace polyscope
diff --git a/include/polyscope/polyscope.h b/include/polyscope/polyscope.h
index 633db17a..c7205399 100644
--- a/include/polyscope/polyscope.h
+++ b/include/polyscope/polyscope.h
@@ -60,7 +60,7 @@ void unshow();
 void frameTick();
 
 // Do shutdown work and de-initialize Polyscope
-void shutdown();
+void shutdown(bool allowMidFrameShutdown=false);
 
 // Returns true if the user has tried to exit the window at the OS level, e.g clicking the close button. Useful for
 // deciding when to exit your control loop when using frameTick()
diff --git a/include/polyscope/render/engine.h b/include/polyscope/render/engine.h
index e5eb8349..3d71e8c0 100644
--- a/include/polyscope/render/engine.h
+++ b/include/polyscope/render/engine.h
@@ -442,6 +442,7 @@ class Engine {
   virtual ~Engine();
 
   // High-level control
+  virtual void shutdown() {};
   virtual void checkError(bool fatal = false) = 0;
   void buildEngineGui();
 
diff --git a/include/polyscope/render/mock_opengl/mock_gl_engine.h b/include/polyscope/render/mock_opengl/mock_gl_engine.h
index 360e06a4..df2651c7 100644
--- a/include/polyscope/render/mock_opengl/mock_gl_engine.h
+++ b/include/polyscope/render/mock_opengl/mock_gl_engine.h
@@ -325,6 +325,7 @@ class MockGLEngine : public Engine {
 
   // High-level control
   void initialize();
+  virtual void shutdown() override;
   void checkError(bool fatal = false) override;
 
   void swapDisplayBuffers() override;
diff --git a/include/polyscope/render/opengl/gl_engine_egl.h b/include/polyscope/render/opengl/gl_engine_egl.h
index 24d93ef3..a57f8863 100644
--- a/include/polyscope/render/opengl/gl_engine_egl.h
+++ b/include/polyscope/render/opengl/gl_engine_egl.h
@@ -38,6 +38,7 @@ class GLEngineEGL : public GLEngine {
 
   // High-level control
   void initialize();
+  virtual void shutdown() override;
   void swapDisplayBuffers() override;
   void checkError(bool fatal = false) override;
 
diff --git a/include/polyscope/render/opengl/gl_engine_glfw.h b/include/polyscope/render/opengl/gl_engine_glfw.h
index 88c38f10..67caddf2 100644
--- a/include/polyscope/render/opengl/gl_engine_glfw.h
+++ b/include/polyscope/render/opengl/gl_engine_glfw.h
@@ -48,6 +48,7 @@ class GLEngineGLFW : public GLEngine {
 
   // High-level control
   void initialize();
+  virtual void shutdown() override;
   void swapDisplayBuffers() override;
 
   // === Windowing and framework things
diff --git a/include/polyscope/slice_plane.h b/include/polyscope/slice_plane.h
index 2316a7f2..f1286011 100644
--- a/include/polyscope/slice_plane.h
+++ b/include/polyscope/slice_plane.h
@@ -111,6 +111,7 @@ class SlicePlane {
 
 SlicePlane* addSceneSlicePlane(bool initiallyVisible = false);
 void removeLastSceneSlicePlane();
+void removeAllSlicePlanes();
 void buildSlicePlaneGUI();
 
 // flag to open the slice plane menu after adding a slice plane
diff --git a/src/messages.cpp b/src/messages.cpp
index fca039a4..e556f88c 100644
--- a/src/messages.cpp
+++ b/src/messages.cpp
@@ -235,7 +235,7 @@ void terminatingError(std::string message) {
   pushContext(func, false);
 
   // Quit the program
-  shutdown();
+  shutdown(true);
   std::exit(-1);
 }
 
@@ -281,4 +281,6 @@ void showDelayedWarnings() {
   }
 }
 
+void clearMessages() { warningMessages.clear(); }
+
 } // namespace polyscope
diff --git a/src/polyscope.cpp b/src/polyscope.cpp
index b26dec14..575f8e2b 100644
--- a/src/polyscope.cpp
+++ b/src/polyscope.cpp
@@ -934,14 +934,30 @@ bool windowRequestsClose() {
   return false;
 }
 
-void shutdown() {
+void shutdown(bool allowMidFrameShutdown) {
+
+  if (!allowMidFrameShutdown && contextStack.size() > 1) {
+    terminatingError("shutdown() was called mid-frame (e.g. in a per-frame callback, or UI element). This is not "
+                     "permitted, shutdown() may only be called when the main loop is not executing.");
+  }
 
-  // TODO should we make an effort to destruct everything here?
   if (options::usePrefsFile) {
     writePrefsFile();
   }
 
-  render::engine->shutdownImGui();
+  // Clear out all structures and other scene objects
+  removeAllStructures();
+  removeAllGroups();
+  removeAllSlicePlanes();
+  clearMessages();
+  state::userCallback = nullptr;
+
+  // Shut down the render engine
+  render::engine->shutdown();
+  delete render::engine;
+  render::engine = nullptr;
+  state::backend = "";
+  state::initialized = false;
 }
 
 bool registerStructure(Structure* s, bool replaceIfPresent) {
diff --git a/src/render/mock_opengl/mock_gl_engine.cpp b/src/render/mock_opengl/mock_gl_engine.cpp
index 6b33aef2..0e6ce5c0 100644
--- a/src/render/mock_opengl/mock_gl_engine.cpp
+++ b/src/render/mock_opengl/mock_gl_engine.cpp
@@ -33,11 +33,8 @@ namespace polyscope {
 namespace render {
 namespace backend_openGL_mock {
 
-
-MockGLEngine* glEngine = nullptr; // alias for engine pointer
-
 void initializeRenderEngine() {
-  glEngine = new MockGLEngine();
+  MockGLEngine* glEngine = new MockGLEngine();
   engine = glEngine;
   glEngine->initialize();
   engine->allocateGlobalBuffersAndPrograms();
@@ -874,7 +871,7 @@ void GLShaderProgram::assignBufferToVAO(GLShaderAttribute& a) {
 void GLShaderProgram::createBuffer(GLShaderAttribute& a) {
 
   // generate the buffer if needed
-  std::shared_ptr<AttributeBuffer> newBuff = glEngine->generateAttributeBuffer(a.type, a.arrayCount);
+  std::shared_ptr<AttributeBuffer> newBuff = engine->generateAttributeBuffer(a.type, a.arrayCount);
   std::shared_ptr<GLAttributeBuffer> engineNewBuff = std::dynamic_pointer_cast<GLAttributeBuffer>(newBuff);
   if (!engineNewBuff) throw std::invalid_argument("buffer type cast failed");
   a.buff = engineNewBuff;
@@ -1581,6 +1578,11 @@ void MockGLEngine::initializeImGui() {
   configureImGui();
 }
 
+void MockGLEngine::shutdown() {
+  checkError();
+  shutdownImGui();
+}
+
 void MockGLEngine::shutdownImGui() { ImGui::DestroyContext(); }
 
 void MockGLEngine::swapDisplayBuffers() {}
diff --git a/src/render/opengl/gl_engine.cpp b/src/render/opengl/gl_engine.cpp
index 477cdac9..f028686c 100644
--- a/src/render/opengl/gl_engine.cpp
+++ b/src/render/opengl/gl_engine.cpp
@@ -38,8 +38,6 @@ namespace render {
 
 namespace backend_openGL3 {
 
-GLEngine* glEngine = nullptr; // alias for global engine pointer
-
 // == Map enums to native values
 
 // clang-format off
@@ -1345,7 +1343,7 @@ void GLShaderProgram::createBuffer(GLShaderAttribute& a) {
   if (a.location == -1) return;
 
   // generate the buffer if needed
-  std::shared_ptr<AttributeBuffer> newBuff = glEngine->generateAttributeBuffer(a.type, a.arrayCount);
+  std::shared_ptr<AttributeBuffer> newBuff = engine->generateAttributeBuffer(a.type, a.arrayCount);
   std::shared_ptr<GLAttributeBuffer> engineNewBuff = std::dynamic_pointer_cast<GLAttributeBuffer>(newBuff);
   if (!engineNewBuff) throw std::invalid_argument("buffer type cast failed");
   a.buff = engineNewBuff;
diff --git a/src/render/opengl/gl_engine_egl.cpp b/src/render/opengl/gl_engine_egl.cpp
index 76a957a0..81a0c3cf 100644
--- a/src/render/opengl/gl_engine_egl.cpp
+++ b/src/render/opengl/gl_engine_egl.cpp
@@ -18,9 +18,6 @@ namespace polyscope {
 namespace render {
 namespace backend_openGL3 {
 
-GLEngineEGL* glEngineEGL = nullptr; // alias for global engine pointer
-extern GLEngine* glEngine;          // defined in gl_engine.h
-
 namespace { // anonymous helpers
 
 void checkEGLError(bool fatal = true) {
@@ -116,10 +113,8 @@ void checkEGLError(bool fatal = true) {
 
 void initializeRenderEngine_egl() {
 
-  glEngineEGL = new GLEngineEGL(); // create the new global engine object
-
-  engine = glEngineEGL; // we keep a few copies of this pointer with various types
-  glEngine = glEngineEGL;
+  GLEngineEGL* glEngineEGL = new GLEngineEGL(); // create the new global engine object
+  engine = glEngineEGL;
 
   // initialize
   glEngineEGL->initialize();
@@ -128,9 +123,7 @@ void initializeRenderEngine_egl() {
 }
 
 GLEngineEGL::GLEngineEGL() {}
-GLEngineEGL::~GLEngineEGL() {
-  // eglTerminate(eglDisplay) // TODO handle termination
-}
+GLEngineEGL::~GLEngineEGL() {}
 
 void GLEngineEGL::initialize() {
 
@@ -239,6 +232,15 @@ void GLEngineEGL::initializeImGui() {
   configureImGui();
 }
 
+void GLEngineEGL::shutdown() {
+  checkError();
+  shutdownImGui();
+
+  eglMakeCurrent(eglDisplay, EGL_NO_SURFACE, EGL_NO_SURFACE, EGL_NO_CONTEXT);
+  eglDestroyContext(eglDisplay, eglContext);
+  eglTerminate(eglDisplay);
+}
+
 void GLEngineEGL::shutdownImGui() { ImGui::DestroyContext(); }
 
 void GLEngineEGL::ImGuiNewFrame() {
diff --git a/src/render/opengl/gl_engine_glfw.cpp b/src/render/opengl/gl_engine_glfw.cpp
index 4eede7aa..585309c3 100644
--- a/src/render/opengl/gl_engine_glfw.cpp
+++ b/src/render/opengl/gl_engine_glfw.cpp
@@ -17,15 +17,11 @@ namespace polyscope {
 namespace render {
 namespace backend_openGL3 {
 
-GLEngineGLFW* glEngineGLFW = nullptr; // alias for global engine pointer
-extern GLEngine* glEngine;            // defined in gl_engine.h
-
 void initializeRenderEngine_glfw() {
 
-  glEngineGLFW = new GLEngineGLFW(); // create the new global engine object
+  GLEngineGLFW* glEngineGLFW = new GLEngineGLFW(); // create the new global engine object
 
   engine = glEngineGLFW; // we keep a few copies of this pointer with various types
-  glEngine = glEngineGLFW;
 
   // initialize
   glEngineGLFW->initialize();
@@ -119,6 +115,15 @@ void GLEngineGLFW::initializeImGui() {
   configureImGui();
 }
 
+
+void GLEngineGLFW::shutdown() {
+  checkError();
+  shutdownImGui();
+  glfwDestroyWindow(mainWindow);
+  glfwTerminate();
+}
+
+
 void GLEngineGLFW::shutdownImGui() {
   // ImGui shutdown things
   ImGui_ImplOpenGL3_Shutdown();
diff --git a/src/slice_plane.cpp b/src/slice_plane.cpp
index cca6cf88..d12731fd 100644
--- a/src/slice_plane.cpp
+++ b/src/slice_plane.cpp
@@ -37,6 +37,12 @@ void removeLastSceneSlicePlane() {
   }
 }
 
+void removeAllSlicePlanes() {
+  while(!state::slicePlanes.empty()) {
+    removeLastSceneSlicePlane();
+  }
+}
+
 void buildSlicePlaneGUI() {
 
 
diff --git a/test/src/basics_test.cpp b/test/src/basics_test.cpp
index df87c353..afb2aafc 100644
--- a/test/src/basics_test.cpp
+++ b/test/src/basics_test.cpp
@@ -84,6 +84,12 @@ TEST_F(PolyscopeTest, Unshow) {
   polyscope::state::userCallback = nullptr;
 }
 
+TEST_F(PolyscopeTest, ShutdownAndReinitialize) {
+  polyscope::shutdown();
+  SetUpTestSuite();
+  polyscope::show(3);
+}
+
 // Make sure that creating an empty buffer does not throw errors
 TEST_F(PolyscopeTest, EmptyBuffer) {