diff --git a/spec/spec-helper.coffee b/spec/spec-helper.coffee
index 6004189c0..7f99d9c2b 100644
--- a/spec/spec-helper.coffee
+++ b/spec/spec-helper.coffee
@@ -82,7 +82,6 @@ beforeEach ->
 
   spyOn(atom, 'saveSync')
   atom.syntax.clearGrammarOverrides()
-  atom.config.clearScopedSettings()
 
   spy = spyOn(atom.packages, 'resolvePackagePath').andCallFake (packageName) ->
     if specPackageName and packageName is specPackageName
diff --git a/src/config.coffee b/src/config.coffee
index 0fb61f286..f751ce63a 100644
--- a/src/config.coffee
+++ b/src/config.coffee
@@ -707,7 +707,7 @@ class Config
       .join(' ')
     @scopedSettingsStore.getPropertyValue(scopeChain, keyPath)
 
-  # TODO: figure out how to change / remove this. The return value is awkward. 
+  # TODO: figure out how to change / remove this. The return value is awkward.
   # * language mode uses it for one thing.
   # * autocomplete uses it for editor.completions
   settingsForScopeDescriptor: (scopeDescriptor, keyPath) ->
@@ -718,9 +718,6 @@ class Config
       .join(' ')
     @scopedSettingsStore.getProperties(scopeChain, keyPath)
 
-  clearScopedSettings: ->
-    @scopedSettingsStore = new ScopedPropertyStore
-
 # Base schema enforcers. These will coerce raw input into the specified type,
 # and will throw an error when the value cannot be coerced. Throwing the error
 # will indicate that the value should not be set.
diff --git a/src/syntax.coffee b/src/syntax.coffee
index 852b48656..02f3e1c5d 100644
--- a/src/syntax.coffee
+++ b/src/syntax.coffee
@@ -47,10 +47,6 @@ class Syntax extends GrammarRegistry
     deprecate 'atom.config.addScopedDefaults() now returns a disposable you can call .dispose() on'
     atom.config.scopedSettingsStore.removeProperties(name)
 
-  clearProperties: ->
-    deprecate 'A direct (but private) replacement is available at atom.config.clearScopedSettings().'
-    atom.config.clearScopedSettings()
-
   getProperty: (scope, keyPath) ->
     deprecate 'A direct (but private) replacement is available at atom.config.getRawScopedValue().'
     atom.config.getRawScopedValue(scope, keyPath)