diff --git a/app/browser/windows.js b/app/browser/windows.js
index 9fdb4636b59..621328fa1c5 100644
--- a/app/browser/windows.js
+++ b/app/browser/windows.js
@@ -147,11 +147,37 @@ const updatePinnedTabs = (win, appState) => {
   }
 }
 
+function refocusFocusedWindow () {
+  const focusedWindow = BrowserWindow.getFocusedWindow()
+  if (focusedWindow) {
+    if (shouldDebugWindowEvents) {
+      console.log('focusing on window', focusedWindow.id)
+    }
+    focusedWindow.focus()
+  }
+}
+
 function showDeferredShowWindow (win) {
-  if (shouldDebugWindowEvents) {
-    console.log(`Window [${win.id}] showDeferredShowWindow`)
+  // were we asked to make the window active / foreground?
+  const shouldShowInactive = win.webContents.browserWindowOptions.inactive
+  if (shouldShowInactive) {
+    // we were asked NOT to show the window active.
+    // we should maintain focus on the window which already has it
+    if (shouldDebugWindowEvents) {
+      console.log('showing deferred window inactive', win.id)
+    }
+    win.showInactive()
+    // Whilst the window will not have focus, it will potentially be
+    // on top of the window which already had focus,
+    // so re-focus the focused window.
+    setImmediate(refocusFocusedWindow)
+  } else {
+    // we were asked to show the window active
+    if (shouldDebugWindowEvents) {
+      console.log('showing deferred window active', win.id)
+    }
+    win.show()
   }
-  win.show()
   if (win.__shouldFullscreen) {
     // this timeout helps with an issue that
     // when a user is loading from state, and
@@ -160,6 +186,9 @@ function showDeferredShowWindow (win) {
     // spaces because macOS has switched away from the desktop space
     setTimeout(() => {
       win.setFullScreen(true)
+      if (shouldShowInactive) {
+        setImmediate(refocusFocusedWindow)
+      }
     }, 100)
   } else if (win.__shouldMaximize) {
     win.maximize()
diff --git a/app/index.js b/app/index.js
index 597f218585a..5388932c3b0 100644
--- a/app/index.js
+++ b/app/index.js
@@ -208,6 +208,7 @@ app.on('ready', () => {
         appActions.newWindow()
       }
     } else {
+      const lastIndex = loadedPerWindowImmutableState.size - 1
       loadedPerWindowImmutableState
         .sort((a, b) => {
           let comparison = 0
@@ -222,8 +223,12 @@ app.on('ready', () => {
 
           return comparison
         })
-        .forEach((wndState) => {
-          appActions.newWindow(undefined, undefined, wndState)
+        .forEach((wndState, i) => {
+          const isLastWindow = i === lastIndex
+          if (CmdLine.shouldDebugWindowEvents && isLastWindow) {
+            console.log(`The restored window which should get focus has ${wndState.get('frames').size} frames`)
+          }
+          appActions.newWindow(undefined, isLastWindow ? undefined : { inactive: true }, wndState, true)
         })
     }
     process.emit(messages.APP_INITIALIZED)
diff --git a/js/entry.js b/js/entry.js
index bac1ef427bc..bf7e249ddcd 100644
--- a/js/entry.js
+++ b/js/entry.js
@@ -77,6 +77,9 @@ ipc.on(messages.INITIALIZE_WINDOW, (e, mem) => {
   const windowValue = message.windowValue
 
   currentWindow.setWindowId(windowValue.id)
+  if (process.env.NODE_ENV === 'development') {
+    console.debug(`This Window's ID is:`, windowValue.id)
+  }
   const newState = Immutable.fromJS(message.windowState) || windowStore.getState()
 
   appStoreRenderer.state = Immutable.fromJS(message.appState)
diff --git a/js/stores/windowStore.js b/js/stores/windowStore.js
index c539d1a33f9..c6db850db7c 100644
--- a/js/stores/windowStore.js
+++ b/js/stores/windowStore.js
@@ -2,8 +2,6 @@
  * License, v. 2.0. If a copy of the MPL was not distributed with this file,
  * You can obtain one at http://mozilla.org/MPL/2.0/. */
 
-/* global performance */
-
 const appDispatcher = require('../dispatcher/appDispatcher')
 const EventEmitter = require('events').EventEmitter
 const appActions = require('../actions/appActions')
@@ -752,21 +750,18 @@ const doAction = (action) => {
         }
         break
       }
-    case windowConstants.WINDOW_ON_WINDOW_UPDATE:
     case appConstants.APP_WINDOW_READY:
-      {
-        const oldInfo = windowState.get('windowInfo', Immutable.Map())
-        let windowValue = makeImmutable(action.windowValue)
-
-        if (windowValue.get('focused')) {
-          windowValue = windowValue.set('focusTime', performance.timing.navigationStart + performance.now())
-        }
-        windowState = windowState.set('windowInfo', oldInfo.merge(windowValue))
-        break
-      }
     case appConstants.APP_WINDOW_UPDATED:
     case appConstants.APP_WINDOW_RESIZED:
-      windowState = windowState.set('windowInfo', action.windowValue)
+      let windowValue = makeImmutable(action.windowValue)
+      const oldInfo = windowState.get('windowInfo', Immutable.Map())
+      // detect if window is newly focused
+      if (windowValue.get('focused') && !oldInfo.get('focused')) {
+        // record time of focus so we can make sure the window
+        // z-index is restored on app-restart
+        windowValue = windowValue.set('focusTime', new Date().getTime())
+      }
+      windowState = windowState.set('windowInfo', oldInfo.merge(windowValue))
       break
     case windowConstants.WINDOW_TAB_MOVE_INCREMENTAL_REQUESTED:
       const sourceFrame = frameStateUtil.getActiveFrame(windowState)
diff --git a/test/unit/lib/fakeWindow.js b/test/unit/lib/fakeWindow.js
index 436268c6b99..ba2701afbfd 100644
--- a/test/unit/lib/fakeWindow.js
+++ b/test/unit/lib/fakeWindow.js
@@ -12,6 +12,7 @@ function FakeWindow (id) {
   this.webContents = Object.assign(new EventEmitter())
   this.webContents.send = this.webContents.emit
   this._isVisible = false
+  this.webContents.browserWindowOptions = { }
 }
 
 util.inherits(FakeWindow, EventEmitter)