diff --git a/Common/GPU/OpenGL/GLRenderManager.h b/Common/GPU/OpenGL/GLRenderManager.h
index e2d132726f..2a7c290f37 100644
--- a/Common/GPU/OpenGL/GLRenderManager.h
+++ b/Common/GPU/OpenGL/GLRenderManager.h
@@ -110,6 +110,9 @@ public:
 class GLRProgram {
 public:
 	~GLRProgram() {
+		if (deleteCallback_) {
+			deleteCallback_(deleteParam_);
+		}
 		if (program) {
 			glDeleteProgram(program);
 		}
@@ -162,6 +165,15 @@ public:
 		return loc;
 	}
 
+	void SetDeleteCallback(void(*cb)(void *), void *p) {
+		deleteCallback_ = cb;
+		deleteParam_ = p;
+	}
+
+private:
+	void(*deleteCallback_)(void *) = nullptr;
+	void *deleteParam_ = nullptr;
+
 	std::unordered_map<std::string, UniformInfo> uniformCache_;
 };
 
diff --git a/GPU/GLES/ShaderManagerGLES.cpp b/GPU/GLES/ShaderManagerGLES.cpp
index 5cb0ba71f6..79a63be54c 100644
--- a/GPU/GLES/ShaderManagerGLES.cpp
+++ b/GPU/GLES/ShaderManagerGLES.cpp
@@ -212,8 +212,17 @@ LinkedShader::LinkedShader(GLRenderManager *render, VShaderID VSID, Shader *vs,
 	dirtyUniforms = DIRTY_ALL_UNIFORMS;
 }
 
-LinkedShader::~LinkedShader() {
+void LinkedShader::Delete() {
+	program->SetDeleteCallback([](void *thiz) {
+		LinkedShader *ls = (LinkedShader *)thiz;
+		delete ls;
+	}, this);
 	render_->DeleteProgram(program);
+	program = nullptr;
+}
+
+LinkedShader::~LinkedShader() {
+	_assert_(program == nullptr);
 }
 
 // Utility
@@ -691,7 +700,7 @@ ShaderManagerGLES::~ShaderManagerGLES() {
 void ShaderManagerGLES::Clear() {
 	DirtyLastShader();
 	for (auto iter = linkedShaderCache_.begin(); iter != linkedShaderCache_.end(); ++iter) {
-		delete iter->ls;
+		iter->ls->Delete();
 	}
 	fsCache_.Iterate([&](const FShaderID &key, Shader *shader) {
 		delete shader;
diff --git a/GPU/GLES/ShaderManagerGLES.h b/GPU/GLES/ShaderManagerGLES.h
index a768ff35a1..b37604ba5d 100644
--- a/GPU/GLES/ShaderManagerGLES.h
+++ b/GPU/GLES/ShaderManagerGLES.h
@@ -42,6 +42,7 @@ public:
 
 	void use(const ShaderID &VSID);
 	void UpdateUniforms(const ShaderID &VSID, bool useBufferedRendering, const ShaderLanguageDesc &shaderLanguage);
+	void Delete();
 
 	GLRenderManager *render_;
 	Shader *vs_;