diff --git a/src/components/Tree/UiTree.js b/src/components/Tree/UiTree.js
index b309e9c4..9fdc21e2 100644
--- a/src/components/Tree/UiTree.js
+++ b/src/components/Tree/UiTree.js
@@ -10,7 +10,8 @@ module.exports = React.createClass({
   propTypes: {
     tree: React.PropTypes.object.isRequired,
     paddingLeft: React.PropTypes.number,
-    renderNode: React.PropTypes.func.isRequired
+    renderNode: React.PropTypes.func.isRequired,
+    onCollapse: React.PropTypes.func,
   },
 
   getDefaultProps() {
@@ -230,8 +231,7 @@ module.exports = React.createClass({
       tree: tree
     });
 
-    // Don't push updates as collapsing is separated from store state
-    // this.change(tree);
+    if(this.props.onCollapse) this.props.onCollapse(node.id, node.collapsed);
   },
 
   // buildTreeNumbering(tree) {
diff --git a/src/scenes/DocumentScene/DocumentScene.js b/src/scenes/DocumentScene/DocumentScene.js
index 4606f1ad..04dbcc8d 100644
--- a/src/scenes/DocumentScene/DocumentScene.js
+++ b/src/scenes/DocumentScene/DocumentScene.js
@@ -3,7 +3,9 @@ import { toJS } from 'mobx';
 import { Link, browserHistory } from 'react-router';
 import { observer } from 'mobx-react';
 
-import DocumentSceneStore from './DocumentSceneStore';
+import DocumentSceneStore, {
+  DOCUMENT_PREFERENCES
+} from './DocumentSceneStore';
 
 import Layout, { HeaderAction } from 'components/Layout';
 import AtlasPreviewLoading from 'components/AtlasPreviewLoading';
@@ -29,7 +31,7 @@ class DocumentScene extends React.Component {
 
   constructor(props) {
     super(props);
-    this.store = new DocumentSceneStore();
+    this.store = new DocumentSceneStore(JSON.parse(localStorage[DOCUMENT_PREFERENCES]));
   }
 
   componentDidMount = () => {
@@ -77,10 +79,6 @@ class DocumentScene extends React.Component {
     );
   }
 
-  handleChange = (tree) => {
-    this.store.updateNavigationTree(tree);
-  }
-
   render() {
     const doc = this.store.document;
     const allowDelete = doc && doc.atlas.type === 'atlas' &&
@@ -127,11 +125,12 @@ class DocumentScene extends React.Component {
             { this.store.isAtlas ? (
               <div className={ styles.sidebar }>
                 <Tree
-                  paddingLeft={10}
-                  tree={ toJS(doc.atlas.navigationTree) }
-                  onChange={this.handleChange}
-                  isNodeCollapsed={this.isNodeCollapsed}
-                  renderNode={this.renderNode}
+                  paddingLeft={ 10 }
+                  tree={ toJS(this.store.atlasTree) }
+                  onChange={ this.store.updateNavigationTree  }
+                  onCollapse={ this.store.onNodeCollapse }
+                  isNodeCollapsed={ this.isNodeCollapsed }
+                  renderNode={ this.renderNode }
                 />
               </div>
             ) : null }
diff --git a/src/scenes/DocumentScene/DocumentSceneStore.js b/src/scenes/DocumentScene/DocumentSceneStore.js
index 3a269e17..dbd41716 100644
--- a/src/scenes/DocumentScene/DocumentSceneStore.js
+++ b/src/scenes/DocumentScene/DocumentSceneStore.js
@@ -1,10 +1,15 @@
 import _isEqual from 'lodash/isEqual';
-import { observable, action, computed, runInAction, toJS } from 'mobx';
+import _indexOf from 'lodash/indexOf';
+import _without from 'lodash/without';
+import { observable, action, computed, runInAction, toJS, autorun } from 'mobx';
 import { client } from 'utils/ApiClient';
 import { browserHistory } from 'react-router';
 
+const DOCUMENT_PREFERENCES = 'DOCUMENT_PREFERENCES';
+
 class DocumentSceneStore {
   @observable document;
+  @observable collapsedNodes = [];
 
   @observable isFetching = true;
   @observable updatingContent = false;
@@ -18,6 +23,24 @@ class DocumentSceneStore {
       this.document.atlas.type === 'atlas';
   }
 
+  @computed get atlasTree() {
+    if (this.document.atlas.type !== 'atlas') return;
+    let tree = this.document.atlas.navigationTree;
+
+    const collapseNodes = (node) => {
+      if (this.collapsedNodes.includes(node.id)) {
+        node.collapsed = true;
+      }
+      node.children = node.children.map(childNode => {
+        return collapseNodes(childNode);
+      })
+
+      return node;
+    };
+
+    return collapseNodes(toJS(tree));
+  }
+
   /* Actions */
 
   @action fetchDocument = async (id, softLoad) => {
@@ -71,6 +94,36 @@ class DocumentSceneStore {
     }
     this.updatingStructure = false;
   }
+
+  @action onNodeCollapse = (nodeId, collapsed) => {
+    if (_indexOf(this.collapsedNodes, nodeId) >= 0) {
+      this.collapsedNodes = _without(this.collapsedNodes, nodeId);
+    } else {
+      this.collapsedNodes.push(nodeId);
+    }
+  }
+
+  // General
+
+  persistSettings = () => {
+    localStorage[DOCUMENT_PREFERENCES] = JSON.stringify({
+      collapsedNodes: toJS(this.collapsedNodes),
+    });
+  }
+
+  constructor(settings) {
+    // Rehydrate settings
+    this.collapsedNodes = settings.collapsedNodes;
+
+    // Persist settings to localStorage
+    // TODO: This could be done more selectively
+    autorun(() => {
+      this.persistSettings();
+    });
+  }
 };
 
 export default DocumentSceneStore;
+export {
+  DOCUMENT_PREFERENCES,
+};