diff --git a/.changeset/chatty-rice-hunt.md b/.changeset/chatty-rice-hunt.md
new file mode 100644
index 00000000000..58969cbde6c
--- /dev/null
+++ b/.changeset/chatty-rice-hunt.md
@@ -0,0 +1,6 @@
+---
+"app-builder-lib": patch
+"electron-builder": patch
+---
+
+fix: correct native dependency tree mismatch in app-builder rebuild
diff --git a/packages/app-builder-lib/src/packager.ts b/packages/app-builder-lib/src/packager.ts
index cbecdf4c5c5..8fb8d38d544 100644
--- a/packages/app-builder-lib/src/packager.ts
+++ b/packages/app-builder-lib/src/packager.ts
@@ -133,8 +133,8 @@ export class Packager {
 
   private nodeDependencyInfo = new Map<string, Lazy<Array<any>>>()
 
-  getNodeDependencyInfo(platform: Platform | null): Lazy<Array<NodeModuleInfo | NodeModuleDirInfo>> {
-    let key = ""
+  getNodeDependencyInfo(platform: Platform | null, flatten: boolean = true): Lazy<Array<NodeModuleInfo | NodeModuleDirInfo>> {
+    let key = "" + flatten.toString()
     let excludedDependencies: Array<string> | null = null
     if (platform != null && this.framework.getExcludedDependencies != null) {
       excludedDependencies = this.framework.getExcludedDependencies(platform)
@@ -145,7 +145,7 @@ export class Packager {
 
     let result = this.nodeDependencyInfo.get(key)
     if (result == null) {
-      result = createLazyProductionDeps(this.appDir, excludedDependencies)
+      result = createLazyProductionDeps(this.appDir, excludedDependencies, flatten)
       this.nodeDependencyInfo.set(key, result)
     }
     return result
@@ -543,7 +543,7 @@ export class Packager {
         frameworkInfo,
         platform: platform.nodeName,
         arch: Arch[arch],
-        productionDeps: this.getNodeDependencyInfo(null) as Lazy<Array<NodeModuleDirInfo>>,
+        productionDeps: this.getNodeDependencyInfo(null, false) as Lazy<Array<NodeModuleDirInfo>>,
       })
     }
   }
diff --git a/packages/app-builder-lib/src/util/packageDependencies.ts b/packages/app-builder-lib/src/util/packageDependencies.ts
index d7e00a2aaf9..907c452ec59 100644
--- a/packages/app-builder-lib/src/util/packageDependencies.ts
+++ b/packages/app-builder-lib/src/util/packageDependencies.ts
@@ -1,15 +1,16 @@
 import { Lazy } from "lazy-val"
 import { executeAppBuilderAsJson } from "./appBuilder"
 
-export function createLazyProductionDeps(projectDir: string, excludedDependencies: Array<string> | null) {
+export function createLazyProductionDeps<T extends boolean>(projectDir: string, excludedDependencies: Array<string> | null, flatten: T) {
   return new Lazy(async () => {
-    const args = ["node-dep-tree", "--flatten", "--dir", projectDir]
+    const args = ["node-dep-tree", "--dir", projectDir]
+    if (flatten) args.push("--flatten")
     if (excludedDependencies != null) {
       for (const name of excludedDependencies) {
         args.push("--exclude-dep", name)
       }
     }
-    return executeAppBuilderAsJson<Array<any>>(args)
+    return executeAppBuilderAsJson<Array<T extends true ? NodeModuleInfo : NodeModuleDirInfo>>(args)
   })
 }
 
diff --git a/packages/electron-builder/src/cli/install-app-deps.ts b/packages/electron-builder/src/cli/install-app-deps.ts
index ae7779fb535..30f506bd7ae 100644
--- a/packages/electron-builder/src/cli/install-app-deps.ts
+++ b/packages/electron-builder/src/cli/install-app-deps.ts
@@ -62,7 +62,7 @@ export async function installAppDeps(args: any) {
       frameworkInfo: { version, useCustomDist: true },
       platform: args.platform,
       arch: args.arch,
-      productionDeps: createLazyProductionDeps(appDir, null),
+      productionDeps: createLazyProductionDeps(appDir, null, false),
     },
     appDir !== projectDir
   )