diff --git a/spec/config-spec.coffee b/spec/config-spec.coffee
index 324db9d8a..01a2eca51 100644
--- a/spec/config-spec.coffee
+++ b/spec/config-spec.coffee
@@ -97,7 +97,7 @@ describe "Config", ->
         atom.config.addScopedSettings("default", ".source.coffee", foo: bar: baz: 42)
         expect(atom.config.getDefault('.source.coffee', 'foo.bar.baz')).toBe 42
 
-        atom.config.set('.source.coffee', 'foo.bar.baz', 55)
+        atom.config.set('foo.bar.baz', 55, scopeSelector: '.source.coffee')
         expect(atom.config.getDefault('.source.coffee', 'foo.bar.baz')).toBe 42
 
   describe ".isDefault(keyPath)", ->
@@ -118,7 +118,7 @@ describe "Config", ->
         atom.config.addScopedSettings("default", ".source.coffee", foo: bar: baz: 42)
         expect(atom.config.isDefault('.source.coffee', 'foo.bar.baz')).toBe true
 
-        atom.config.set('.source.coffee', 'foo.bar.baz', 55)
+        atom.config.set('foo.bar.baz', 55, scopeSelector: '.source.coffee')
         expect(atom.config.isDefault('.source.coffee', 'foo.bar.baz')).toBe false
 
   describe ".setDefaults(keyPath)", ->
@@ -174,7 +174,7 @@ describe "Config", ->
     describe "when scoped settings are used", ->
       it "restores the global default when no scoped default set", ->
         atom.config.setDefaults("foo", bar: baz: 10)
-        atom.config.set('.source.coffee', 'foo.bar.baz', 55)
+        atom.config.set('foo.bar.baz', 55, scopeSelector: '.source.coffee')
         expect(atom.config.get(['.source.coffee'], 'foo.bar.baz')).toBe 55
 
         atom.config.restoreDefault('.source.coffee', 'foo.bar.baz')
@@ -183,8 +183,8 @@ describe "Config", ->
       it "restores the scoped default when a scoped default is set", ->
         atom.config.setDefaults("foo", bar: baz: 10)
         atom.config.addScopedSettings("default", ".source.coffee", foo: bar: baz: 42)
-        atom.config.set('.source.coffee', 'foo.bar.baz', 55)
-        atom.config.set('.source.coffee', 'foo.bar.ok', 100)
+        atom.config.set('foo.bar.baz', 55, scopeSelector: '.source.coffee')
+        atom.config.set('foo.bar.ok', 100, scopeSelector: '.source.coffee')
         expect(atom.config.get(['.source.coffee'], 'foo.bar.baz')).toBe 55
 
         atom.config.restoreDefault('.source.coffee', 'foo.bar.baz')
@@ -194,7 +194,7 @@ describe "Config", ->
       it "calls ::save()", ->
         atom.config.setDefaults("foo", bar: baz: 10)
         atom.config.addScopedSettings("default", ".source.coffee", foo: bar: baz: 42)
-        atom.config.set('.source.coffee', 'foo.bar.baz', 55)
+        atom.config.set('foo.bar.baz', 55, scopeSelector: '.source.coffee')
         atom.config.save.reset()
 
         atom.config.restoreDefault('.source.coffee', 'foo.bar.baz')
@@ -216,8 +216,8 @@ describe "Config", ->
         jasmine.unspy atom.config, 'save'
 
         atom.config.setDefaults("foo", bar: baz: 10)
-        atom.config.set('.source.coffee', 'foo.bar.baz', 55)
-        atom.config.set('.source.coffee', 'foo.bar.zfoo', 20)
+        atom.config.set('foo.bar.baz', 55, scopeSelector: '.source.coffee')
+        atom.config.set('foo.bar.zfoo', 20, scopeSelector: '.source.coffee')
         CSON.writeFileSync.reset()
         expect(atom.config.get(['.source.coffee'], 'foo.bar.baz')).toBe 55
 
@@ -239,7 +239,7 @@ describe "Config", ->
 
       it "does not call ::save when the value is already at the default", ->
         atom.config.setDefaults("foo", bar: baz: 10)
-        atom.config.set('.source.coffee', 'foo.bar.baz', 55)
+        atom.config.set('foo.bar.baz', 55)
         atom.config.save.reset()
 
         atom.config.restoreDefault('.source.coffee', 'foo.bar.ok')
@@ -353,9 +353,9 @@ describe "Config", ->
 
     describe "when scoped settings are defined", ->
       it 'writes out explicitly set config settings', ->
-        atom.config.set('.source.ruby', 'foo.bar', 'ruby')
-        atom.config.set('.source.ruby', 'foo.omg', 'wow')
-        atom.config.set('.source.coffee', 'foo.bar', 'coffee')
+        atom.config.set('foo.bar', 'ruby', scopeSelector: '.source.ruby')
+        atom.config.set('foo.omg', 'wow', scopeSelector: '.source.ruby')
+        atom.config.set('foo.bar', 'coffee', scopeSelector: '.source.coffee')
 
         CSON.writeFileSync.reset()
         atom.config.save()
@@ -1125,7 +1125,7 @@ describe "Config", ->
       describe 'setting priority', ->
         describe 'when package settings are added after user settings', ->
           it "returns the user's setting because the user's setting has higher priority", ->
-            atom.config.set(".source.coffee", "foo.bar.baz", 100)
+            atom.config.set("foo.bar.baz", 100, scopeSelector: ".source.coffee")
             atom.config.addScopedSettings("some-package", ".source.coffee", foo: bar: baz: 1)
             expect(atom.config.get([".source.coffee"], "foo.bar.baz")).toBe 100
 
@@ -1137,7 +1137,7 @@ describe "Config", ->
 
         expect(atom.config.get([".source.coffee", ".string.quoted.double.coffee"], "foo.bar.baz")).toBe 42
 
-        expect(atom.config.set(".source.coffee .string.quoted.double.coffee", "foo.bar.baz", 100)).toBe true
+        expect(atom.config.set("foo.bar.baz", 100, scopeSelector: ".source.coffee .string.quoted.double.coffee")).toBe true
         expect(atom.config.get([".source.coffee", ".string.quoted.double.coffee"], "foo.bar.baz")).toBe 100
 
     describe ".removeScopedSettingsForName(name)", ->
diff --git a/spec/text-editor-component-spec.coffee b/spec/text-editor-component-spec.coffee
index 7e0810ceb..31a11b54d 100644
--- a/spec/text-editor-component-spec.coffee
+++ b/spec/text-editor-component-spec.coffee
@@ -2577,9 +2577,9 @@ describe "TextEditorComponent", ->
 
     describe 'soft wrap settings', ->
       beforeEach ->
-        atom.config.set '.source.coffee', 'editor.softWrap', true
-        atom.config.set '.source.coffee', 'editor.preferredLineLength', 17
-        atom.config.set '.source.coffee', 'editor.softWrapAtPreferredLineLength', true
+        atom.config.set 'editor.softWrap', true, scopeSelector: '.source.coffee'
+        atom.config.set 'editor.preferredLineLength', 17, scopeSelector: '.source.coffee'
+        atom.config.set 'editor.softWrapAtPreferredLineLength', true, scopeSelector: '.source.coffee'
 
         editor.setEditorWidthInChars(20)
         coffeeEditor.setEditorWidthInChars(20)
@@ -2589,18 +2589,18 @@ describe "TextEditorComponent", ->
         expect(coffeeEditor.lineTextForScreenRow(3)).toEqual '    return items '
 
       it 'updates the wrapped lines when editor.preferredLineLength changes', ->
-        atom.config.set '.source.coffee', 'editor.preferredLineLength', 20
+        atom.config.set 'editor.preferredLineLength', 20, scopeSelector: '.source.coffee'
         expect(coffeeEditor.lineTextForScreenRow(2)).toEqual '    return items if '
 
       it 'updates the wrapped lines when editor.softWrapAtPreferredLineLength changes', ->
-        atom.config.set '.source.coffee', 'editor.softWrapAtPreferredLineLength', false
+        atom.config.set 'editor.softWrapAtPreferredLineLength', false, scopeSelector: '.source.coffee'
         expect(coffeeEditor.lineTextForScreenRow(2)).toEqual '    return items if '
 
       it 'updates the wrapped lines when editor.softWrap changes', ->
-        atom.config.set '.source.coffee', 'editor.softWrap', false
+        atom.config.set 'editor.softWrap', false, scopeSelector: '.source.coffee'
         expect(coffeeEditor.lineTextForScreenRow(2)).toEqual '    return items if items.length <= 1'
 
-        atom.config.set '.source.coffee', 'editor.softWrap', true
+        atom.config.set 'editor.softWrap', true, scopeSelector: '.source.coffee'
         expect(coffeeEditor.lineTextForScreenRow(3)).toEqual '    return items '
 
       it 'updates the wrapped lines when the grammar changes', ->
@@ -2628,11 +2628,11 @@ describe "TextEditorComponent", ->
           tab: 'F'
           cr: 'E'
 
-        atom.config.set '.source.js', 'editor.showInvisibles', true
-        atom.config.set '.source.js', 'editor.invisibles', jsInvisibles
+        atom.config.set 'editor.showInvisibles', true, scopeSelector: '.source.js'
+        atom.config.set 'editor.invisibles', jsInvisibles, scopeSelector: '.source.js'
 
-        atom.config.set '.source.coffee', 'editor.showInvisibles', false
-        atom.config.set '.source.coffee', 'editor.invisibles', coffeeInvisibles
+        atom.config.set 'editor.showInvisibles', false, scopeSelector: '.source.coffee'
+        atom.config.set 'editor.invisibles', coffeeInvisibles, scopeSelector: '.source.coffee'
 
         editor.setText " a line with tabs\tand spaces \n"
         nextAnimationFrame()
@@ -2648,7 +2648,7 @@ describe "TextEditorComponent", ->
       it "re-renders the invisibles when the invisible settings change", ->
         jsGrammar = editor.getGrammar()
         editor.setGrammar(coffeeEditor.getGrammar())
-        atom.config.set '.source.coffee', 'editor.showInvisibles', true
+        atom.config.set 'editor.showInvisibles', true, scopeSelector: '.source.coffee'
         nextAnimationFrame()
         expect(component.lineNodeForScreenRow(0).textContent).toBe "#{coffeeInvisibles.space}a line with tabs#{coffeeInvisibles.tab}and spaces#{coffeeInvisibles.space}#{coffeeInvisibles.eol}"
 
@@ -2657,7 +2657,7 @@ describe "TextEditorComponent", ->
           space: 'E'
           tab: 'W'
           cr: 'I'
-        atom.config.set '.source.coffee', 'editor.invisibles', newInvisibles
+        atom.config.set 'editor.invisibles', newInvisibles, scopeSelector: '.source.coffee'
         nextAnimationFrame()
         expect(component.lineNodeForScreenRow(0).textContent).toBe "#{newInvisibles.space}a line with tabs#{newInvisibles.tab}and spaces#{newInvisibles.space}#{newInvisibles.eol}"
 
@@ -2667,8 +2667,8 @@ describe "TextEditorComponent", ->
 
     describe 'editor.showIndentGuide', ->
       beforeEach ->
-        atom.config.set '.source.js', 'editor.showIndentGuide', true
-        atom.config.set '.source.coffee', 'editor.showIndentGuide', false
+        atom.config.set 'editor.showIndentGuide', true, scopeSelector: '.source.js'
+        atom.config.set 'editor.showIndentGuide', false, scopeSelector: '.source.coffee'
 
       it "has an 'indent-guide' class when scoped editor.showIndentGuide is true, but not when scoped editor.showIndentGuide is false", ->
         line1LeafNodes = getLeafNodes(component.lineNodeForScreenRow(1))
@@ -2689,7 +2689,7 @@ describe "TextEditorComponent", ->
         expect(line1LeafNodes[0].classList.contains('indent-guide')).toBe true
         expect(line1LeafNodes[1].classList.contains('indent-guide')).toBe false
 
-        atom.config.set '.source.js', 'editor.showIndentGuide', false
+        atom.config.set 'editor.showIndentGuide', false, scopeSelector: '.source.js'
 
         line1LeafNodes = getLeafNodes(component.lineNodeForScreenRow(1))
         expect(line1LeafNodes[0].textContent).toBe '  '
diff --git a/spec/text-editor-spec.coffee b/spec/text-editor-spec.coffee
index b84b3b944..c70991f38 100644
--- a/spec/text-editor-spec.coffee
+++ b/spec/text-editor-spec.coffee
@@ -1327,7 +1327,7 @@ describe "TextEditor", ->
           coffeeEditor.selectWordsContainingCursors()
           expect(coffeeEditor.getSelectedBufferRange()).toEqual [[0, 6], [0, 15]]
 
-          atom.config.set '.source.coffee', 'editor.nonWordCharacters', 'qusort'
+          atom.config.set 'editor.nonWordCharacters', 'qusort', scopeSelector: '.source.coffee'
 
           coffeeEditor.setCursorBufferPosition [0, 9]
           coffeeEditor.selectWordsContainingCursors()
@@ -3276,7 +3276,7 @@ describe "TextEditor", ->
         atom.packages.unloadPackages()
 
       it 'returns correct values based on the scope of the set grammars', ->
-        atom.config.set '.source.coffee', 'editor.tabLength', 6
+        atom.config.set 'editor.tabLength', 6, scopeSelector: '.source.coffee'
 
         expect(editor.getTabLength()).toBe 2
         expect(coffeeEditor.getTabLength()).toBe 6
@@ -3298,12 +3298,12 @@ describe "TextEditor", ->
         expect(editor.getTabLength()).toBe 2
         expect(editor.tokenizedLineForScreenRow(5).tokens[0].firstNonWhitespaceIndex).toBe 2
 
-        atom.config.set '.source.js', 'editor.tabLength', 6
+        atom.config.set 'editor.tabLength', 6, scopeSelector: '.source.js'
         expect(editor.getTabLength()).toBe 6
         expect(editor.tokenizedLineForScreenRow(5).tokens[0].firstNonWhitespaceIndex).toBe 6
 
       it 'updates the tab length when the grammar changes', ->
-        atom.config.set '.source.coffee', 'editor.tabLength', 6
+        atom.config.set 'editor.tabLength', 6, scopeSelector: '.source.coffee'
 
         expect(editor.getTabLength()).toBe 2
         expect(editor.tokenizedLineForScreenRow(5).tokens[0].firstNonWhitespaceIndex).toBe 2
@@ -3473,8 +3473,8 @@ describe "TextEditor", ->
           atom.project.open('coffee.coffee', autoIndent: false).then (o) -> coffeeEditor = o
 
         runs ->
-          atom.config.set('.source.js', 'editor.autoIndent', true)
-          atom.config.set('.source.coffee', 'editor.autoIndent', false)
+          atom.config.set('editor.autoIndent', true, scopeSelector: '.source.js')
+          atom.config.set('editor.autoIndent', false, scopeSelector: '.source.coffee')
 
       afterEach: ->
         atom.packages.deactivatePackages()
diff --git a/src/config.coffee b/src/config.coffee
index dcad15b56..66f4f9433 100644
--- a/src/config.coffee
+++ b/src/config.coffee
@@ -504,13 +504,20 @@ class Config
   # Returns a {Boolean}
   # * `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: (scopeSelector, keyPath, value) ->
-    if arguments.length < 3
-      value = keyPath
-      keyPath = scopeSelector
-      scopeSelector = undefined
+  set: ->
+    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.
+      """
+      scopeSelector = arguments[0]
+      keyPath = arguments[1]
+      value = arguments[2]
+    else
+      [keyPath, value, options] = arguments
+      scopeSelector = options?.scopeSelector
 
-    unless value == undefined
+    unless value is undefined
       try
         value = @makeValueConformToSchema(keyPath, value)
       catch e