diff --git a/src/lib/settings.html b/src/lib/settings.html
index 77eccef2..7e4c4288 100644
--- a/src/lib/settings.html
+++ b/src/lib/settings.html
@@ -38,6 +38,8 @@ subject to an additional IP rights grant found at http://polymer.github.io/PATEN
       var useNativeCustomElements = (!window.CustomElements ||
         window.CustomElements.useNative);
 
+      var usePolyfillProto = !useNativeCustomElements && !Object.__proto__;
+
       return {
         wantShadow: wantShadow,
         hasShadow: hasShadow,
@@ -45,7 +47,8 @@ subject to an additional IP rights grant found at http://polymer.github.io/PATEN
         useShadow: useShadow,
         useNativeShadow: useShadow && nativeShadow,
         useNativeImports: useNativeImports,
-        useNativeCustomElements: useNativeCustomElements
+        useNativeCustomElements: useNativeCustomElements,
+        usePolyfillProto: usePolyfillProto
       };
     })()
   };
diff --git a/src/standard/configure.html b/src/standard/configure.html
index 2fc292b4..b994b003 100644
--- a/src/standard/configure.html
+++ b/src/standard/configure.html
@@ -9,7 +9,7 @@ subject to an additional IP rights grant found at http://polymer.github.io/PATEN
 -->
 
 <script>
-
+(function() {
   /*
     Process inputs efficiently via a configure lifecycle callback.
     Configure is called top-down, host before local dom. Users should
@@ -41,6 +41,8 @@ subject to an additional IP rights grant found at http://polymer.github.io/PATEN
   directly (on-foo-changed).
   */
 
+  var usePolyfillProto = Polymer.Settings.usePolyfillProto;
+
   Polymer.Base._addFeature({
 
     // storage for configuration
@@ -114,8 +116,14 @@ subject to an additional IP rights grant found at http://polymer.github.io/PATEN
     _configureProperties: function(properties, config) {
       for (var i in properties) {
         var c = properties[i];
-        // don't accept undefined values
-        if (c.value !== undefined) {
+        // Allow properties set before upgrade on the instance 
+        // to override default values. This allows late upgrade + an early set
+        // to not b0rk accessors on the prototype.
+        // Perf testing has shown `hasOwnProperty` to be ok here.
+        if (!usePolyfillProto && this.hasOwnProperty(i)) {
+          config[i] = this[i];
+          delete this[i];
+        } else if (c.value !== undefined) {
           var value = c.value;
           if (typeof value == 'function') {
             // pass existing config values (this._config) to value function
@@ -217,4 +225,5 @@ subject to an additional IP rights grant found at http://polymer.github.io/PATEN
 
   });
 
+})();
 </script>
diff --git a/test/unit/configure.html b/test/unit/configure.html
index 996dc62c..dc125a89 100644
--- a/test/unit/configure.html
+++ b/test/unit/configure.html
@@ -103,6 +103,36 @@ subject to an additional IP rights grant found at http://polymer.github.io/PATEN
       assert.equal(e.$.child.attrNumberChanged.getCall(0).args[0], 42);
     });
 
+    test('pre-register property assignment does not break getters and setters', function() {
+      // don't test if __proto__ is polyfilled (IE10); cannot be fixed in this case.
+      if (Polymer.Settings.usePolyfillProto) {
+        return;
+      }
+      var x = document.createElement('x-late-register');
+      document.body.appendChild(x);
+      // set property
+      x.shouldChange = '1';
+      // now register element
+      Polymer({
+        is: 'x-late-register',
+        properties: {
+          shouldChange : {
+            observer: 'shouldChangeCallback',
+            type: String
+          }
+        },
+        shouldChangeCallback: function() {
+          this.textContent = this.shouldChange;
+        }
+      });
+      CustomElements.takeRecords();
+      assert.equal(x.shouldChange, '1');
+      assert.equal(x.shouldChange, x.textContent);
+      x.shouldChange = '2';
+      assert.equal(x.shouldChange, '2');
+      assert.equal(x.shouldChange, x.textContent);
+      document.body.removeChild(x);
+    });
   });
 
 </script>