diff --git a/spec/config-spec.coffee b/spec/config-spec.coffee
index 0156855d9..31e4f70bc 100644
--- a/spec/config-spec.coffee
+++ b/spec/config-spec.coffee
@@ -110,6 +110,10 @@ describe "Config", ->
       expect(atom.config.save).toHaveBeenCalled()
       expect(observeHandler).toHaveBeenCalledWith 42
 
+    it "does not save when a non-default 'source' is given", ->
+      atom.config.set("foo.bar.baz", 42, source: 'some-other-source', scopeSelector: '.a')
+      expect(atom.config.save).not.toHaveBeenCalled()
+
     it "does not allow a 'source' option without a 'scopeSelector'", ->
       expect(-> atom.config.set("foo", 1, source: [".source.ruby"])).toThrow()
 
diff --git a/src/config.coffee b/src/config.coffee
index 8169b13f2..ef2847015 100644
--- a/src/config.coffee
+++ b/src/config.coffee
@@ -548,6 +548,7 @@ class Config
       [keyPath, value, options] = arguments
       scopeSelector = options?.scopeSelector
       source = options?.source
+      shouldSave = options?.save ? true
 
     if source and not scopeSelector
       throw new Error("::set with a 'source' and no 'sourceSelector' is not yet implemented!")
@@ -565,7 +566,7 @@ class Config
     else
       @setRawValue(keyPath, value)
 
-    @save() unless @configFileHasErrors or options?.save is false
+    @save() if source is @getUserConfigPath() and shouldSave and not @configFileHasErrors
     true
 
   # Essential: Restore the setting at `keyPath` to its default value.