diff --git a/lib/utils/scope-subtree.js b/lib/utils/scope-subtree.js
index 7932d27f81..f99a7fb724 100644
--- a/lib/utils/scope-subtree.js
+++ b/lib/utils/scope-subtree.js
@@ -9,10 +9,22 @@ subject to an additional IP rights grant found at http://polymer.github.io/PATEN
 */
 
 import './boot.js';
+import {wrap} from './wrap.js';
 
 const ShadyDOM = window.ShadyDOM;
 const ShadyCSS = window.ShadyCSS;
 
+/**
+ * Return true if node scope is correct.
+ *
+ * @param {!Element} node Node to check scope
+ * @param {!Node} scope Scope reference
+ * @return {boolean} True if node is in scope
+ */
+function sameScope(node, scope) {
+  return wrap(node).getRootNode() === scope;
+}
+
 /**
  * Ensure that elements in a ShadowDOM container are scoped correctly.
  * This function is only needed when ShadyDOM is used and unpatched DOM APIs are used in third party code.
@@ -38,13 +50,20 @@ export function scopeSubtree(container, shouldObserve = false) {
   }
   // capture correct scope for container
   const containerScope = ScopingShim['scopeForNode'](container);
+  const root = wrap(container).getRootNode();
 
   const scopify = (node) => {
+    if (!sameScope(node, root)) {
+      return;
+    }
     // NOTE: native qSA does not honor scoped DOM, but it is faster, and the same behavior as Polymer v1
     const elements = Array.from(ShadyDOM['nativeMethods']['querySelectorAll'].call(node, '*'));
     elements.push(node);
     for (let i = 0; i < elements.length; i++) {
       const el = elements[i];
+      if (!sameScope(el, root)) {
+        continue;
+      }
       const currentScope = ScopingShim['currentScopeForNode'](el);
       if (currentScope !== containerScope) {
         if (currentScope !== '') {
diff --git a/test/unit/styling-scoped-nopatch.html b/test/unit/styling-scoped-nopatch.html
index b1f82b1fea..2d9426c995 100644
--- a/test/unit/styling-scoped-nopatch.html
+++ b/test/unit/styling-scoped-nopatch.html
@@ -50,6 +50,24 @@
   customElements.define('scope-subtree-element', ScopeSubtreeElement);
 </script>
 
+<script type="module">
+  import {Polymer, html} from '../../polymer-legacy.js';
+  Polymer({
+    is: 'scope-subtree-deep',
+    _template: html`
+      <style>
+        div {
+          border: 20px dotted orange !important;
+        }
+      </style>
+      <div id="target"></div>
+      <div id="container">
+        <scope-subtree-legacy id="other"></scope-subtree-legacy>
+      </div>
+    `,
+  });
+</script>
+
 <test-fixture id="legacy">
   <template>
     <scope-subtree-legacy></scope-subtree-legacy>
@@ -62,6 +80,12 @@
   </template>
 </test-fixture>
 
+<test-fixture id="deep">
+  <template>
+    <scope-subtree-deep></scope-subtree-deep>
+  </template>
+</test-fixture>
+
 <script type="module">
   import { scopeSubtree } from '../../lib/utils/scope-subtree.js';
 
@@ -127,6 +151,22 @@
       assertComputed(div, '10px');
       assertComputed(innerDiv, '10px');
     });
+
+    suite('scopeSubtree containment', function() {
+      let el;
+      setup(function() {
+        el = fixture('deep');
+      });
+      test('scopeSubtree does not modify other elements\' trees', function() {
+        const container = el.$.container;
+        const deepContainer = el.$.other.$.container;
+        const deep = document.createElement('div');
+        deepContainer.appendChild(deep);
+        el.$.other.scopeSubtree(deepContainer);
+        el.scopeSubtree(container);
+        assertComputed(deep, '10px');
+      });
+    });
   });
 </script>
 </body>