diff --git a/packages/runtime-core/src/hmr.ts b/packages/runtime-core/src/hmr.ts
index 4191a34f8..8f443de0c 100644
--- a/packages/runtime-core/src/hmr.ts
+++ b/packages/runtime-core/src/hmr.ts
@@ -31,11 +31,17 @@ export interface HMRRuntime {
 // Note: for a component to be eligible for HMR it also needs the __hmrId option
 // to be set so that its instances can be registered / removed.
 if (__DEV__) {
-  getGlobalThis().__VUE_HMR_RUNTIME__ = {
-    createRecord: tryWrap(createRecord),
-    rerender: tryWrap(rerender),
-    reload: tryWrap(reload),
-  } as HMRRuntime
+  const g = getGlobalThis()
+  // vite-plugin-vue/issues/644, #13202
+  // custom-element libraries bundle Vue to simplify usage outside Vue projects but
+  // it overwrite __VUE_HMR_RUNTIME__, causing HMR to break.
+  if (!g.__VUE_HMR_RUNTIME__) {
+    g.__VUE_HMR_RUNTIME__ = {
+      createRecord: tryWrap(createRecord),
+      rerender: tryWrap(rerender),
+      reload: tryWrap(reload),
+    } as HMRRuntime
+  }
 }
 
 const map: Map<