diff --git a/atom.sh b/atom.sh
index 57d7f71e6..768ab72b9 100755
--- a/atom.sh
+++ b/atom.sh
@@ -24,7 +24,11 @@ case $(basename $0) in
     ;;
 esac
 
-export ATOM_DISABLE_SHELLING_OUT_FOR_ENVIRONMENT=true
+# Only set the ATOM_DISABLE_SHELLING_OUT_FOR_ENVIRONMENT env var if it hasn't been set.
+if [ -z "$ATOM_DISABLE_SHELLING_OUT_FOR_ENVIRONMENT" ]
+then
+  export ATOM_DISABLE_SHELLING_OUT_FOR_ENVIRONMENT=true
+fi
 
 ATOM_ADD=false
 ATOM_NEW_WINDOW=false
diff --git a/resources/linux/atom.desktop.in b/resources/linux/atom.desktop.in
index 43074179d..f028eba23 100644
--- a/resources/linux/atom.desktop.in
+++ b/resources/linux/atom.desktop.in
@@ -2,7 +2,7 @@
 Name=<%= appName %>
 Comment=<%= description %>
 GenericName=Text Editor
-Exec=<%= installDir %>/bin/<%= appFileName %> %F
+Exec=env ATOM_DISABLE_SHELLING_OUT_FOR_ENVIRONMENT=false <%= installDir %>/bin/<%= appFileName %> %F
 Icon=<%= iconPath %>
 Type=Application
 StartupNotify=true
diff --git a/src/update-process-env.js b/src/update-process-env.js
index 20d937d96..a7e2622dd 100644
--- a/src/update-process-env.js
+++ b/src/update-process-env.js
@@ -51,7 +51,9 @@ function shouldGetEnvFromShell (env) {
     return false
   }
 
-  if (env.ATOM_DISABLE_SHELLING_OUT_FOR_ENVIRONMENT || process.env.ATOM_DISABLE_SHELLING_OUT_FOR_ENVIRONMENT) {
+  const disableSellingOut = env.ATOM_DISABLE_SHELLING_OUT_FOR_ENVIRONMENT || process.env.ATOM_DISABLE_SHELLING_OUT_FOR_ENVIRONMENT
+
+  if (disableSellingOut === 'true') {
     return false
   }