diff --git a/spec/config-spec.coffee b/spec/config-spec.coffee
index 3f5e2e814..ea274e6d8 100644
--- a/spec/config-spec.coffee
+++ b/spec/config-spec.coffee
@@ -486,6 +486,7 @@ describe "Config", ->
 
       atom.config.set('foo.bar.baz', "value 1")
       expect(observeHandler).toHaveBeenCalledWith("value 1")
+      advanceClock(100) # complete pending save that was requested in ::set
 
       observeHandler.reset()
       atom.config.loadUserConfig()
@@ -772,6 +773,22 @@ describe "Config", ->
           expect(warnSpy).toHaveBeenCalled()
           expect(warnSpy.mostRecentCall.args[0]).toContain "foo.int"
 
+      describe "when there is a pending save", ->
+        it "does not change the config settings", ->
+          fs.writeFileSync atom.config.configFilePath, "'*': foo: bar: 'baz'"
+
+          atom.config.set("foo.bar", "quux")
+          atom.config.loadUserConfig()
+          expect(atom.config.get("foo.bar")).toBe "quux"
+
+          advanceClock(100)
+          expect(atom.config.save.callCount).toBe 1
+
+          expect(atom.config.get("foo.bar")).toBe "quux"
+          atom.config.loadUserConfig()
+          expect(atom.config.get("foo.bar")).toBe "baz"
+
+
     describe ".observeUserConfig()", ->
       updatedHandler = null
 
diff --git a/src/browser/application.coffee b/src/browser/application.coffee
index 69098031a..e9846e383 100644
--- a/src/browser/application.coffee
+++ b/src/browser/application.coffee
@@ -1,10 +1,10 @@
-Config = require '../config'
 AtomWindow = require './atom-window'
 BrowserWindow = require 'browser-window'
 WindowManager = require './window-manager'
 ApplicationMenu = require './application-menu'
 AutoUpdateManager = require './auto-update-manager'
 NylasProtocolHandler = require './nylas-protocol-handler'
+SharedFileManager = require './shared-file-manager'
 
 _ = require 'underscore'
 fs = require 'fs-plus'
@@ -73,13 +73,16 @@ class Application
 
     global.application = this
 
+    @sharedFileManager = new SharedFileManager()
+    @nylasProtocolHandler = new NylasProtocolHandler(@resourcePath, @safeMode)
+
+    Config = require '../config'
     @config = new Config({configDirPath, @resourcePath})
     @config.load()
 
     @windowManager = new WindowManager({@resourcePath, @config, @devMode, @safeMode})
     @autoUpdateManager = new AutoUpdateManager(@version, @config, @specMode)
     @applicationMenu = new ApplicationMenu(@version)
-    @nylasProtocolHandler = new NylasProtocolHandler(@resourcePath, @safeMode)
     @_databasePhase = 'setup'
 
     @listenForArgumentsFromNewProcess()
diff --git a/src/browser/shared-file-manager.coffee b/src/browser/shared-file-manager.coffee
new file mode 100644
index 000000000..ad2906eff
--- /dev/null
+++ b/src/browser/shared-file-manager.coffee
@@ -0,0 +1,15 @@
+class SharedFileManager
+
+  constructor: ->
+    @_inflight = {}
+
+  processWillWriteFile: (filePath) ->
+    @_inflight[filePath] += 1
+
+  processDidWriteFile: (filePath) ->
+    @_inflight[filePath] -= 1
+
+  processCanReadFile: (filePath) ->
+    !@_inflight[filePath] or @_inflight[filePath] is 0
+
+module.exports = SharedFileManager
diff --git a/src/config.coffee b/src/config.coffee
index cdd8b0651..ec0057fa4 100644
--- a/src/config.coffee
+++ b/src/config.coffee
@@ -13,6 +13,11 @@ Color = require './color'
 ScopedPropertyStore = require 'scoped-property-store'
 ScopeDescriptor = require './scope-descriptor'
 
+if global.application
+  app = global.application
+else
+  app = require('remote').getGlobal('application')
+
 # Essential: Used to access all of Atom's configuration details.
 #
 # An instance of this class is always available as the `atom.config` global.
@@ -334,9 +339,17 @@ class Config
     @configFilePath = fs.resolve(@configDirPath, 'config', ['json', 'cson'])
     @configFilePath ?= path.join(@configDirPath, 'config.cson')
     @transactDepth = 0
+    @savePending = false
 
-    @debouncedSave = _.debounce(@save, 100)
+    @requestLoad = _.debounce(@loadUserConfig, 100)
     @debouncedLoad = _.debounce(@loadUserConfig, 100)
+    @requestSave = =>
+      @savePending = true
+      debouncedSave.call(this)
+    save = =>
+      @savePending = false
+      @save()
+    debouncedSave = _.debounce(save, 100)
 
   ###
   Section: Config Subscription
@@ -607,7 +620,7 @@ class Config
     else
       @setRawValue(keyPath, value)
 
-    @debouncedSave() if source is @getUserConfigPath() and shouldSave and not @configFileHasErrors
+    @requestSave() if source is @getUserConfigPath() and shouldSave and not @configFileHasErrors
     true
 
   # Essential: Restore the setting at `keyPath` to its default value.
@@ -637,7 +650,7 @@ class Config
           _.setValueForKeyPath(settings, keyPath, undefined)
           settings = withoutEmptyObjects(settings)
           @set(null, settings, {scopeSelector, source, priority: @priorityForSource(source)}) if settings?
-          @debouncedSave()
+          @requestSave()
       else
         @scopedSettingsStore.removePropertiesForSourceAndSelector(source, scopeSelector)
         @emitChangeEvent()
@@ -816,14 +829,20 @@ class Config
     fs.copySync(templateConfigDirPath, @configDirPath)
 
   loadUserConfig: ->
+    manager = app.sharedFileManager
+    if not manager.processCanReadFile(@configFilePath)
+      @requestLoad()
+      return
+
     unless fs.existsSync(@configFilePath)
       fs.makeTreeSync(path.dirname(@configFilePath))
       CSON.writeFileSync(@configFilePath, {})
 
     try
-      userConfig = CSON.readFileSync(@configFilePath)
-      @resetUserSettings(userConfig)
-      @configFileHasErrors = false
+      unless @savePending
+        userConfig = CSON.readFileSync(@configFilePath)
+        @resetUserSettings(userConfig)
+        @configFileHasErrors = false
     catch error
       @configFileHasErrors = true
       message = "Failed to load `#{path.basename(@configFilePath)}`"
@@ -840,7 +859,7 @@ class Config
   observeUserConfig: ->
     try
       @watchSubscription ?= pathWatcher.watch @configFilePath, (eventType) =>
-        @debouncedLoad() if eventType is 'change' and @watchSubscription?
+        @requestLoad() if eventType is 'change' and @watchSubscription?
     catch error
       @notifyFailure """
         Unable to watch path: `#{path.basename(@configFilePath)}`. Make sure you have permissions to
@@ -857,9 +876,12 @@ class Config
     console.log(errorMessage, detail)
 
   save: ->
+    manager = app.sharedFileManager
+    manager.processWillWriteFile(@configFilePath)
     allSettings = {'*': @settings}
     allSettings = _.extend allSettings, @scopedSettingsStore.propertiesForSource(@getUserConfigPath())
     CSON.writeFileSync(@configFilePath, allSettings)
+    manager.processDidWriteFile(@configFilePath)
 
   ###
   Section: Private methods managing global settings