diff --git a/spec/config-spec.coffee b/spec/config-spec.coffee
index 189b3daca..b884b3659 100644
--- a/spec/config-spec.coffee
+++ b/spec/config-spec.coffee
@@ -112,6 +112,13 @@ describe "Config", ->
     it "does not allow a 'source' option without a 'scopeSelector'", ->
       expect(-> atom.config.set("foo", 1, source: [".source.ruby"])).toThrow()
 
+    describe "when the key-path is null", ->
+      it "sets the root object", ->
+        expect(atom.config.set(null, editor: tabLength: 6)).toBe true
+        expect(atom.config.get("editor.tabLength")).toBe 6
+        expect(atom.config.set(null, editor: tabLength: 8, scopeSelector: ['.source.js'])).toBe true
+        expect(atom.config.get("editor.tabLength", scope: ['.source.js'])).toBe 8
+
     describe "when the value equals the default value", ->
       it "does not store the value in the user's config", ->
         atom.config.setDefaults "foo",
diff --git a/src/config.coffee b/src/config.coffee
index b237a1e79..a2cc6ad13 100644
--- a/src/config.coffee
+++ b/src/config.coffee
@@ -539,7 +539,7 @@ class Config
   # * `true` if the value was set.
   # * `false` if the value was not able to be coerced to the type specified in the setting's schema.
   set: ->
-    if arguments[0][0] is '.'
+    if arguments[0]?[0] is '.'
       Grim.deprecate """
         Passing a scope selector as the first argument to Config::set is deprecated.
         Pass a `scopeSelector` in an options hash as the final argument instead.
@@ -856,7 +856,10 @@ class Config
     defaultValue = _.valueForKeyPath(@defaultSettings, keyPath)
     value = undefined if _.isEqual(defaultValue, value)
 
-    _.setValueForKeyPath(@settings, keyPath, value)
+    if keyPath?
+      _.setValueForKeyPath(@settings, keyPath, value)
+    else
+      @settings = value
     @emitChangeEvent()
 
   observeKeyPath: (keyPath, options, callback) ->