diff --git a/src/sandbox/index.ts b/src/sandbox/index.ts
index 26e3eee2c..8138630ce 100644
--- a/src/sandbox/index.ts
+++ b/src/sandbox/index.ts
@@ -25,11 +25,6 @@ import SnapshotSandbox from './snapshotSandbox';
  * @param singular
  */
 export function createSandbox(appName: string, elementGetter: () => HTMLElement | ShadowRoot, singular: boolean) {
-  // mounting freers are one-off and should be re-init at every mounting time
-  let mountingFreers: Freer[] = [];
-
-  let sideEffectsRebuilders: Rebuilder[] = [];
-
   let sandbox: SandBox;
   if (window.Proxy) {
     sandbox = singular ? new LegacySandbox(appName) : new ProxySandbox(appName);
@@ -39,6 +34,10 @@ export function createSandbox(appName: string, elementGetter: () => HTMLElement
 
   // some side effect could be be invoked while bootstrapping, such as dynamic stylesheet injection with style-loader, especially during the development phase
   const bootstrappingFreers = patchAtBootstrapping(appName, elementGetter, sandbox.proxy, singular);
+  // mounting freers are one-off and should be re-init at every mounting time
+  let mountingFreers: Freer[] = [];
+
+  let sideEffectsRebuilders: Rebuilder[] = [];
 
   return {
     proxy: sandbox.proxy,
diff --git a/src/sandbox/patchers/dynamicHeadAppend.ts b/src/sandbox/patchers/dynamicHeadAppend.ts
index c4f15c4ba..ca231e717 100644
--- a/src/sandbox/patchers/dynamicHeadAppend.ts
+++ b/src/sandbox/patchers/dynamicHeadAppend.ts
@@ -271,7 +271,8 @@ function getNewInsertBefore(...args: any[]) {
   };
 }
 
-let patchCount = 0;
+let bootstrappingPatchCount = 0;
+let mountingPatchCount = 0;
 
 /**
  * Just hijack dynamic head append, that could avoid accidentally hijacking the insertion of elements except in head.
@@ -351,17 +352,16 @@ export default function patch(
     );
   }
 
-  if (mounting) {
-    patchCount++;
-  }
+  if (!mounting) bootstrappingPatchCount++;
+  if (mounting) mountingPatchCount++;
 
   return function free() {
-    if (mounting) {
-      patchCount--;
-    }
+    // bootstrap patch just called once but its freer will be called multiple times
+    if (!mounting && bootstrappingPatchCount !== 0) bootstrappingPatchCount--;
+    if (mounting) mountingPatchCount--;
 
     // release the overwrite prototype after all the micro apps unmounted
-    if (patchCount === 0) {
+    if (mountingPatchCount === 0 && bootstrappingPatchCount === 0) {
       HTMLHeadElement.prototype.appendChild = rawHeadAppendChild;
       HTMLHeadElement.prototype.insertBefore = rawHeadInsertBefore;
       HTMLHeadElement.prototype.removeChild = rawHeadRemoveChild;