diff --git a/src/core/core.controller.js b/src/core/core.controller.js
index 5a17d1afb64..d73bb4e4934 100644
--- a/src/core/core.controller.js
+++ b/src/core/core.controller.js
@@ -35,8 +35,13 @@ defaults._set('global', {
 	responsiveAnimationDuration: 0
 });
 
-function mergeScaleConfig(/* objects ... */) {
-	return helpers.merge(helpers.clone(arguments[0]), [].slice.call(arguments, 1), {
+/**
+ * Recursively merge the given config objects as the `scales` options by
+ * incorporating scale defaults in `xAxes` and `yAxes` array items, then
+ * returns a deep copy of the result, thus doesn't alter inputs.
+ */
+function mergeScaleConfig(/* config objects ... */) {
+	return helpers.merge({}, Array.prototype.slice.call(arguments), {
 		merger: function(key, target, source, options) {
 			if (key === 'xAxes' || key === 'yAxes') {
 				var slen = source[key].length;
@@ -70,8 +75,13 @@ function mergeScaleConfig(/* objects ... */) {
 	});
 }
 
-function mergeConfig(/* objects ... */) {
-	return helpers.merge(helpers.clone(arguments[0]), [].slice.call(arguments, 1), {
+/**
+ * Recursively merge the given config objects as the root options by handling
+ * default scale options for the `scales` and `scale` properties, then returns
+ * a deep copy of the result, thus doesn't alter inputs.
+ */
+function mergeConfig(/* config objects ... */) {
+	return helpers.merge({}, Array.prototype.slice.call(arguments), {
 		merger: function(key, target, source, options) {
 			var tval = target[key] || {};
 			var sval = source[key];
diff --git a/test/specs/core.controller.tests.js b/test/specs/core.controller.tests.js
index 62c54b75ce1..819074393b1 100644
--- a/test/specs/core.controller.tests.js
+++ b/test/specs/core.controller.tests.js
@@ -271,6 +271,36 @@ describe('Chart', function() {
 					_jasmineCheckE: 'e2'
 				}));
 		});
+
+		it('should not alter defaults when merging config', function() {
+			var chart = acquireChart({
+				type: 'line',
+				options: {
+					_jasmineCheck: 42,
+					scales: {
+						xAxes: [{
+							id: 'foo',
+							type: 'linear',
+							_jasmineCheck: 42,
+						}],
+						yAxes: [{
+							id: 'bar',
+							type: 'category',
+							_jasmineCheck: 42,
+						}]
+					}
+				}
+			});
+
+			expect(chart.options._jasmineCheck).toBeDefined();
+			expect(chart.scales.foo.options._jasmineCheck).toBeDefined();
+			expect(chart.scales.bar.options._jasmineCheck).toBeDefined();
+
+			expect(Chart.defaults.line._jasmineCheck).not.toBeDefined();
+			expect(Chart.defaults.global._jasmineCheck).not.toBeDefined();
+			expect(Chart.scaleService.defaults.linear._jasmineCheck).not.toBeDefined();
+			expect(Chart.scaleService.defaults.category._jasmineCheck).not.toBeDefined();
+		});
 	});
 
 	describe('config.options.responsive: false', function() {