diff --git a/spec/main-process/atom-application.test.js b/spec/main-process/atom-application.test.js
index 16aef8e27..c49e36b5d 100644
--- a/spec/main-process/atom-application.test.js
+++ b/spec/main-process/atom-application.test.js
@@ -606,6 +606,8 @@ describe('AtomApplication', function () {
     assert(!electron.app.didQuit())
 
     await Promise.all([window1.lastPrepareToUnloadPromise, window2.lastPrepareToUnloadPromise])
+    assert(!electron.app.didQuit())
+    await atomApplication.lastBeforeQuitPromise
     await new Promise(process.nextTick)
     assert(electron.app.didQuit())
   })
@@ -634,6 +636,29 @@ describe('AtomApplication', function () {
     assert(electron.app.didQuit())
   })
 
+  it('closes successfully unloaded windows when quitting', async () => {
+    const atomApplication = buildAtomApplication()
+    const [window1] = await atomApplication.launch(parseCommandLine([]))
+    const [window2] = await atomApplication.launch(parseCommandLine([]))
+    await Promise.all([window1.loadedPromise, window2.loadedPromise])
+    await evalInWebContents(window1.browserWindow.webContents, sendBackToMainProcess => {
+      atom.workspace.getActiveTextEditor().insertText('unsaved text')
+      sendBackToMainProcess()
+    })
+
+    // Choosing "Cancel"
+    mockElectronShowMessageBox({response: 1})
+    electron.app.quit()
+    await atomApplication.lastBeforeQuitPromise
+    assert(atomApplication.getAllWindows().length === 1)
+
+    // Choosing "Don't save"
+    mockElectronShowMessageBox({response: 2})
+    electron.app.quit()
+    await atomApplication.lastBeforeQuitPromise
+    assert(atomApplication.getAllWindows().length === 0)
+  })
+
   function buildAtomApplication (params = {}) {
     const atomApplication = new AtomApplication(Object.assign({
       resourcePath: ATOM_RESOURCE_PATH,
diff --git a/src/main-process/atom-application.js b/src/main-process/atom-application.js
index 8a6d03733..c10895650 100644
--- a/src/main-process/atom-application.js
+++ b/src/main-process/atom-application.js
@@ -437,7 +437,14 @@ class AtomApplication extends EventEmitter {
       if (!this.quitting) {
         this.quitting = true
         event.preventDefault()
-        const windowUnloadPromises = this.getAllWindows().map(window => window.prepareToUnload())
+        const windowUnloadPromises = this.getAllWindows().map(async window => {
+          const unloaded = await window.prepareToUnload()
+          if (unloaded) {
+            window.close()
+            await window.closedPromise
+          }
+          return unloaded
+        })
         const windowUnloadedResults = await Promise.all(windowUnloadPromises)
         if (windowUnloadedResults.every(Boolean)) {
           app.quit()