diff --git a/src/atom-environment.js b/src/atom-environment.js
index 52780e648..45fcb3bbd 100644
--- a/src/atom-environment.js
+++ b/src/atom-environment.js
@@ -223,8 +223,8 @@ class AtomEnvironment {
     })
     this.config.resetUserSettings(userSettings)
 
-    if (projectSettings != null) {
-      this.project.resetProjectSettings(projectSettings)
+    if (projectSettings != null && projectSettings.paths != null || projectSettings.config != null) {
+      this.project.replaceAtomProject(projectSettings)
     }
 
     this.menu.initialize({resourcePath})
diff --git a/src/config.js b/src/config.js
index 5922da368..8c7fd85b7 100644
--- a/src/config.js
+++ b/src/config.js
@@ -1013,6 +1013,7 @@ class Config {
 
   resetProjectSettings (newSettings, options = {}) {
     // Sets the scope and source of all project settings to `path`.
+    newSettings = Object.assign({}, newSettings)
     this.hasCurrentProject = !options.removeProject
     const pathScopedSettings = {}
     pathScopedSettings[PROJECT] = newSettings
diff --git a/src/main-process/atom-application.js b/src/main-process/atom-application.js
index b198b722a..38316497a 100644
--- a/src/main-process/atom-application.js
+++ b/src/main-process/atom-application.js
@@ -856,7 +856,7 @@ class AtomApplication extends EventEmitter {
     }
 
     let openedWindow
-    if (existingWindow && projectSettings == null) {
+    if (existingWindow && projectSettings.paths == null && projectSettings.config == null) {
       openedWindow = existingWindow
       openedWindow.openLocations(locationsToOpen)
       if (openedWindow.isMinimized()) {
diff --git a/src/main-process/atom-window.js b/src/main-process/atom-window.js
index 3f8b7a1af..bd93c9cc4 100644
--- a/src/main-process/atom-window.js
+++ b/src/main-process/atom-window.js
@@ -158,7 +158,7 @@ class AtomWindow extends EventEmitter {
     Object.defineProperty(this.browserWindow, 'loadSettingsJSON', {
       get: () => JSON.stringify(Object.assign({
         userSettings: this.atomApplication.configFile.get(),
-        projectSettings: this.getProjectSettings()
+        projectSettings: this.projectSettings
       }, this.loadSettings)),
       configurable: true
     })
diff --git a/src/main-process/parse-command-line.js b/src/main-process/parse-command-line.js
index 73160ae1c..98b89bb73 100644
--- a/src/main-process/parse-command-line.js
+++ b/src/main-process/parse-command-line.js
@@ -138,14 +138,17 @@ module.exports = function parseCommandLine (processArgs) {
     devMode = true
   }
 
-  let projectSettings
+  let projectSettings = {}
   if (atomProject) {
-    const config = readProjectSettingsSync(atomProject, executedFrom)
-    const paths = config.paths
-    projectSettings = config.config
+    const contents = readProjectSettingsSync(atomProject, executedFrom)
+    const paths = contents.paths
+    const config = contents.config
+    const originPath = atomProject
     if (paths != null) {
       pathsToOpen = pathsToOpen.concat(paths)
     }
+    projectSettings = { originPath, paths, config }
+
   }
 
   if (devMode) {
@@ -198,7 +201,7 @@ const readProjectSettingsSync = (filepath, executedFrom) => {
   try {
     const readPath = path.isAbsolute(filepath) ? filepath : path.join(executedFrom, filepath)
     const contents = CSON.readFileSync(readPath)
-    if (contents.paths || content.config) {
+    if (contents.paths || contents.config) {
       return contents
     }
 
diff --git a/src/project.js b/src/project.js
index 7a5680da0..e660c7e31 100644
--- a/src/project.js
+++ b/src/project.js
@@ -38,6 +38,7 @@ class Project extends Model {
     this.retiredBufferIDs = new Set()
     this.retiredBufferPaths = new Set()
     this.subscriptions = new CompositeDisposable()
+    this.projectFilePath = null
     this.consumeServices(packageManager)
   }
 
@@ -77,14 +78,21 @@ class Project extends Model {
     }
   }
 
-  resetProjectSettings (newSettings) {
-    atom.config.resetProjectSettings(newSettings)
+  // Layers the contents of an atomProject file's config
+  // on top of the current global config. 
+  replaceAtomProject (newSettings) {
+    atom.config.resetProjectSettings(newSettings.config)
+    this.projectFilePath = newSettings.originPath
   }
 
   clearProjectSettings () {
     atom.config.clearProjectSettings()
   }
 
+  getProjectFilePath () {
+    return this.projectFilePath
+  }
+
   /*
   Section: Serialization
   */