diff --git a/src/atom-environment.coffee b/src/atom-environment.coffee
index f4dc49060..6ef46dc2a 100644
--- a/src/atom-environment.coffee
+++ b/src/atom-environment.coffee
@@ -139,7 +139,9 @@ class AtomEnvironment extends Model
 
     @stateStore = new StateStore('AtomEnvironments', 1)
 
-    @stateStore.clear() if clearWindowState
+    if clearWindowState
+      @getStorageFolder().clear()
+      @stateStore.clear()
 
     @deserializers = new DeserializerManager(this)
     @deserializeTimings = {}
diff --git a/src/storage-folder.coffee b/src/storage-folder.coffee
index 06beae56a..327697672 100644
--- a/src/storage-folder.coffee
+++ b/src/storage-folder.coffee
@@ -6,6 +6,14 @@ class StorageFolder
   constructor: (containingPath) ->
     @path = path.join(containingPath, "storage") if containingPath?
 
+  clear: ->
+    return unless @path?
+
+    try
+      fs.removeSync(@path)
+    catch error
+      console.warn "Error deleting #{statePath}", error.stack, error
+
   storeSync: (name, object) ->
     return unless @path?