diff --git a/src/main-process/atom-application.js b/src/main-process/atom-application.js
index 61c44f6fd..a8642b34b 100644
--- a/src/main-process/atom-application.js
+++ b/src/main-process/atom-application.js
@@ -23,6 +23,11 @@ const ConfigSchema = require('../config-schema')
 
 const LocationSuffixRegExp = /(:\d+)(:\d+)?$/
 
+// Increment this when changing the serialization format of `${ATOM_HOME}/storage/application.json` used by
+// AtomApplication::saveCurrentWindowOptions() and AtomApplication::loadPreviousWindowOptions() in a backward-
+// incompatible way.
+const APPLICATION_STATE_VERSION = '1'
+
 const getDefaultPath = () => {
   const editor = atom.workspace.getActiveTextEditor()
   if (!editor || !editor.getPath()) {
@@ -1139,27 +1144,56 @@ class AtomApplication extends EventEmitter {
   async saveCurrentWindowOptions (allowEmpty = false) {
     if (this.quitting) return
 
-    const states = []
-    for (let window of this.getAllWindows()) {
-      if (!window.isSpec) states.push({initialPaths: window.projectRoots})
+    const state = {
+      version: APPLICATION_STATE_VERSION,
+      windows: this.getAllWindows()
+        .filter(window => !window.isSpec)
+        .map(window => ({projectRoots: window.projectRoots}))
     }
-    states.reverse()
+    state.windows.reverse()
 
-    if (states.length > 0 || allowEmpty) {
-      await this.storageFolder.store('application.json', states)
+    if (state.windows.length > 0 || allowEmpty) {
+      await this.storageFolder.store('application.json', state)
       this.emit('application:did-save-state')
     }
   }
 
   async loadPreviousWindowOptions () {
-    const states = await this.storageFolder.load('application.json')
-    if (states) {
-      return states.map(state => ({
-        foldersToOpen: state.initialPaths,
+    const state = await this.storageFolder.load('application.json')
+    if (!state) {
+      return []
+    }
+
+    if (state.version === APPLICATION_STATE_VERSION) {
+      // Atom >=1.36.1
+      // Schema: {version: '1', windows: [{projectRoots: ['<root-dir>', ...]}, ...]}
+      return state.windows.map(each => ({
+        foldersToOpen: each.projectRoots,
         devMode: this.devMode,
         safeMode: this.safeMode
       }))
+    } else if (state.version === undefined) {
+      // Atom <= 1.36.0
+      // Schema: [{initialPaths: ['<root-dir>', ...]}, ...]
+      return await Promise.all(
+        state.map(async windowState => {
+          // Classify each window's initialPaths as directories or non-directories
+          const classifiedPaths = await Promise.all(
+            windowState.initialPaths.map(initialPath => new Promise(resolve => {
+              fs.isDirectory(initialPath, isDir => resolve({initialPath, isDir}))
+            }))
+          )
+
+          // Only accept initialPaths that are existing directories
+          return {
+            foldersToOpen: classifiedPaths.filter(({isDir}) => isDir).map(({initialPath}) => initialPath),
+            devMode: this.devMode,
+            safeMode: this.safeMode
+          }
+        })
+      )
     } else {
+      // Unrecognized version (from a newer Atom?)
       return []
     }
   }