diff --git a/src/application-delegate.js b/src/application-delegate.js
index 8d7981edb..f6bbd6797 100644
--- a/src/application-delegate.js
+++ b/src/application-delegate.js
@@ -325,6 +325,13 @@ class ApplicationDelegate {
     return new Disposable(() => ipcRenderer.removeListener('prepare-to-unload', outerCallback))
   }
 
+  onUnloadAborted (callback) {
+    const outerCallback = (event, message) => callback(event)
+
+    ipcRenderer.on('unload-aborted', outerCallback)
+    return new Disposable(() => ipcRenderer.removeListener('unload-aborted', outerCallback))
+  }
+
   onDidChangeHistoryManager (callback) {
     const outerCallback = (event, message) => callback(event)
 
diff --git a/src/atom-environment.js b/src/atom-environment.js
index 59e4da1f6..b773b4d5b 100644
--- a/src/atom-environment.js
+++ b/src/atom-environment.js
@@ -64,7 +64,7 @@ class AtomEnvironment {
     this.applicationDelegate = params.applicationDelegate
 
     this.nextProxyRequestId = 0
-    this.unloaded = false
+    this.unloading = false
     this.loadTime = null
     this.emitter = new Emitter()
     this.disposables = new CompositeDisposable()
@@ -280,7 +280,7 @@ class AtomEnvironment {
   attachSaveStateListeners () {
     const saveState = _.debounce(() => {
       this.window.requestIdleCallback(() => {
-        if (!this.unloaded) this.saveState({isUnloading: false})
+        if (!this.unloading) this.saveState({isUnloading: false})
       })
     }, this.saveStateDebounceInterval)
     this.document.addEventListener('mousedown', saveState, true)
@@ -775,7 +775,7 @@ class AtomEnvironment {
       await this.stateStore.clear()
     }
 
-    this.unloaded = false
+    this.unloading = false
 
     const updateProcessEnvPromise = this.updateProcessEnvAndTriggerHooks()
 
@@ -812,9 +812,15 @@ class AtomEnvironment {
           projectHasPaths: this.project.getPaths().length > 0
         })
 
-        if (closing) await this.packages.deactivatePackages()
+        if (closing) {
+          this.unloading = true;
+          await this.packages.deactivatePackages()
+        }
         return closing
       }))
+      this.disposables.add(this.applicationDelegate.onUnloadAborted(() => {
+        this.unloading = false
+      }));
 
       this.listenForUpdates()
 
@@ -898,7 +904,6 @@ class AtomEnvironment {
 
     this.storeWindowBackground()
     this.saveBlobStoreSync()
-    this.unloaded = true
   }
 
   saveBlobStoreSync () {
diff --git a/src/main-process/atom-application.js b/src/main-process/atom-application.js
index a9ff4f731..9868d59ce 100644
--- a/src/main-process/atom-application.js
+++ b/src/main-process/atom-application.js
@@ -442,6 +442,7 @@ class AtomApplication extends EventEmitter {
         if (windowUnloadedResults.every(Boolean)) {
           app.quit()
         } else {
+          this.getAllWindows().forEach(window => window.unloadAborted())
           this.quitting = false
         }
       }
diff --git a/src/main-process/atom-window.js b/src/main-process/atom-window.js
index a56679143..16317449e 100644
--- a/src/main-process/atom-window.js
+++ b/src/main-process/atom-window.js
@@ -245,6 +245,10 @@ class AtomWindow extends EventEmitter {
     return this.lastPrepareToUnloadPromise
   }
 
+  unloadAborted () {
+    this.browserWindow.webContents.send('unload-aborted')
+  }
+
   openPath (pathToOpen, initialLine, initialColumn) {
     return this.openLocations([{pathToOpen, initialLine, initialColumn}])
   }