diff --git a/src/workspace-element.coffee b/src/workspace-element.coffee
index ccf165439..5f127d970 100644
--- a/src/workspace-element.coffee
+++ b/src/workspace-element.coffee
@@ -156,9 +156,9 @@ atom.commands.add 'atom-workspace',
   'window:focus-pane-on-left': -> @focusPaneViewOnLeft()
   'window:focus-pane-on-right': -> @focusPaneViewOnRight()
   'window:save-all': -> @getModel().saveAll()
-  'window:toggle-invisibles': -> atom.config.toggle("editor.showInvisibles")
+  'window:toggle-invisibles': -> atom.config.set("editor.showInvisibles", !atom.config.get("editor.showInvisibles"))
   'window:log-deprecation-warnings': -> Grim.logDeprecations()
-  'window:toggle-auto-indent': -> atom.config.toggle("editor.autoIndent")
+  'window:toggle-auto-indent': -> atom.config.set("editor.autoIndent", !atom.config.get("editor.autoIndent"))
   'pane:reopen-closed-item': -> @getModel().reopenItem()
   'core:close': -> @getModel().destroyActivePaneItemOrEmptyPane()
   'core:save': -> @getModel().saveActivePaneItem()