diff --git a/src/atom-environment.js b/src/atom-environment.js
index 45fcb3bbd..760610bf2 100644
--- a/src/atom-environment.js
+++ b/src/atom-environment.js
@@ -223,7 +223,7 @@ class AtomEnvironment {
     })
     this.config.resetUserSettings(userSettings)
 
-    if (projectSettings != null && projectSettings.paths != null || projectSettings.config != null) {
+    if (projectSettings != null && projectSettings.config != null) {
       this.project.replaceAtomProject(projectSettings)
     }
 
diff --git a/src/main-process/parse-command-line.js b/src/main-process/parse-command-line.js
index 98b89bb73..ebfc03bd3 100644
--- a/src/main-process/parse-command-line.js
+++ b/src/main-process/parse-command-line.js
@@ -140,7 +140,7 @@ module.exports = function parseCommandLine (processArgs) {
 
   let projectSettings = {}
   if (atomProject) {
-    const contents = readProjectSettingsSync(atomProject, executedFrom)
+    const contents = Object.assign({}, readProjectSettingsSync(atomProject, executedFrom))
     const paths = contents.paths
     const config = contents.config
     const originPath = atomProject