diff --git a/.idea/dictionaries/develar.xml b/.idea/dictionaries/develar.xml
index 5e2a7ff90fa..f7a5359c01c 100644
--- a/.idea/dictionaries/develar.xml
+++ b/.idea/dictionaries/develar.xml
@@ -31,6 +31,7 @@
       <w>chown</w>
       <w>circleci</w>
       <w>clcerts</w>
+      <w>cleanuped</w>
       <w>cleanuper</w>
       <w>codesigning</w>
       <w>controlfields</w>
diff --git a/packages/electron-builder/src/asarUtil.ts b/packages/electron-builder/src/asarUtil.ts
index d3b0c081362..8c15f509f7b 100644
--- a/packages/electron-builder/src/asarUtil.ts
+++ b/packages/electron-builder/src/asarUtil.ts
@@ -190,10 +190,22 @@ class AsarPackager {
         const fileParent = path.dirname(file)
         const dirNode = this.fs.searchNodeFromPath(fileParent)
         const packageDataPromise = fileIndexToModulePackageData.get(i)
-        let newData: any | null = null
+        let newData: string | null = null
         if (packageDataPromise == null) {
-          if (this.options.extraMetadata != null && file === mainPackageJson) {
-            newData = JSON.stringify(deepAssign(await readJson(file), this.options.extraMetadata), null, 2)
+          if (file === mainPackageJson) {
+            const mainPackageData = await readJson(file)
+            if (this.options.extraMetadata != null) {
+              deepAssign(mainPackageData, this.options.extraMetadata)
+            }
+
+            // https://github.com/electron-userland/electron-builder/issues/1212
+            const serializedDataIfChanged = cleanupPackageJson(mainPackageData)
+            if (serializedDataIfChanged != null) {
+              newData = serializedDataIfChanged
+            }
+            else if (this.options.extraMetadata != null) {
+              newData = JSON.stringify(mainPackageData, null, 2)
+            }
           }
         }
         else {
@@ -352,7 +364,7 @@ function cleanupPackageJson(data: any): any {
   try {
     let changed = false
     for (const prop of Object.getOwnPropertyNames(data)) {
-      if (prop[0] === "_" || prop === "dist" || prop === "gitHead" || prop === "keywords") {
+      if (prop[0] === "_" || prop === "dist" || prop === "gitHead" || prop === "keywords" || prop === "build" || prop === "devDependencies" || prop === "scripts") {
         delete data[prop]
         changed = true
       }
diff --git a/packages/electron-builder/src/platformPackager.ts b/packages/electron-builder/src/platformPackager.ts
index 438920371b9..23e96904296 100644
--- a/packages/electron-builder/src/platformPackager.ts
+++ b/packages/electron-builder/src/platformPackager.ts
@@ -128,7 +128,11 @@ export abstract class PlatformPackager<DC extends PlatformSpecificBuildOptions>
     log(`Packaging for ${platformName} ${Arch[arch]} using electron ${this.info.electronVersion} to ${path.relative(this.projectDir, appOutDir)}`)
 
     const appDir = this.info.appDir
-    const ignoreFiles = new Set([path.resolve(this.info.projectDir, outDir), path.resolve(this.info.projectDir, this.buildResourcesDir)])
+    const ignoreFiles = new Set([path.resolve(this.info.projectDir, outDir),
+      path.resolve(this.info.projectDir, this.buildResourcesDir),
+      path.resolve(this.info.projectDir, "electron-builder.yml"),
+      path.resolve(this.info.projectDir, "electron-builder.json"),
+      path.resolve(this.info.projectDir, "electron-builder.json5")])
     if (this.info.isPrepackedAppAsar) {
       await unpackElectron(this, appOutDir, platformName, Arch[arch], this.info.electronVersion)
     }
diff --git a/test/out/__snapshots__/extraMetadataTest.js.snap b/test/out/__snapshots__/extraMetadataTest.js.snap
index 05841269787..f7972aa26b8 100644
--- a/test/out/__snapshots__/extraMetadataTest.js.snap
+++ b/test/out/__snapshots__/extraMetadataTest.js.snap
@@ -1,20 +1,6 @@
 exports[`test extra metadata 1`] = `
 Object {
   "author": "Foo Bar <foo@example.com>",
-  "build": Object {
-    "appId": "org.electron-builder.testApp",
-    "compression": "store",
-    "electronVersion": "1.4.12",
-    "iconUrl": "https://raw.githubusercontent.com/szwacz/electron-boilerplate/master/resources/windows/icon.ico",
-    "linux": Object {
-      "category": "Development",
-      "packageCategory": "devel",
-    },
-    "mac": Object {
-      "category": "your.app.category.type",
-    },
-    "npmRebuild": false,
-  },
   "description": "Test Application (test quite \" #378)",
   "foo": Object {
     "bar": 12,
diff --git a/test/out/__snapshots__/globTest.js.snap b/test/out/__snapshots__/globTest.js.snap
index 4e683aaf138..146b061bbac 100644
--- a/test/out/__snapshots__/globTest.js.snap
+++ b/test/out/__snapshots__/globTest.js.snap
@@ -6,7 +6,7 @@ Object {
 
 exports[`test outside link 1`] = `
 Object {
-  "offset": "5290",
+  "offset": "4877",
   "size": 4,
 }
 `;
diff --git a/test/src/extraMetadataTest.ts b/test/src/extraMetadataTest.ts
index 4a38a64ceec..bf308ac892b 100644
--- a/test/src/extraMetadataTest.ts
+++ b/test/src/extraMetadataTest.ts
@@ -18,6 +18,8 @@ test.ifDevOrLinuxCi("extra metadata", app({
   },
 }, {
   projectDirCreated: projectDir => modifyPackageJson(projectDir, data => {
+    data.scripts = {}
+    data.devDependencies = {"foo": "boo"}
     data.foo = {
       bar: 42,
       existingProp: 22,
diff --git a/test/src/linux/linuxPackagerTest.ts b/test/src/linux/linuxPackagerTest.ts
index 857076f44f8..a9e59d58a00 100755
--- a/test/src/linux/linuxPackagerTest.ts
+++ b/test/src/linux/linuxPackagerTest.ts
@@ -3,6 +3,7 @@ import { remove, readFile, rename } from "fs-extra-p"
 import * as path from "path"
 import { Platform, build } from "electron-builder"
 import { assertThat } from "../helpers/fileAssert"
+import { ELECTRON_VERSION } from "../helpers/config"
 
 test.ifDevOrLinuxCi("AppImage", app({targets: Platform.LINUX.createTarget()}))
 
@@ -38,6 +39,10 @@ test.ifNotWindows("icons from ICNS", app({targets: Platform.LINUX.createTarget()
     await build({
       targets: Platform.LINUX.createTarget(),
       projectDir: projectDir,
+      config: {
+        electronVersion: ELECTRON_VERSION,
+        compression: "store",
+      }
     })
 
     await assertThat(path.join(projectDir, "dist")).isDirectory()