diff --git a/lib/arborist/load-actual.js b/lib/arborist/load-actual.js
index 6c59a064b..43a9e65ca 100644
--- a/lib/arborist/load-actual.js
+++ b/lib/arborist/load-actual.js
@@ -27,6 +27,7 @@ const _cache = Symbol('nodeLoadingCache')
 const _loadActualVirtually = Symbol('loadActualVirtually')
 const _loadActualActually = Symbol('loadActualActually')
 const _transplant = Symbol('transplant')
+const _transplantFilter = Symbol('transplantFilter')
 
 const _filter = Symbol('filter')
 const _global = Symbol.for('global')
@@ -69,8 +70,14 @@ module.exports = cls => class ActualLoader extends cls {
     if (this.actualTree)
       return this.actualTree
 
-    const { global = false, filter = () => true, root = null } = options
+    const {
+      global = false,
+      filter = () => true,
+      root = null,
+      transplantFilter = () => true,
+    } = options
     this[_filter] = filter
+    this[_transplantFilter] = transplantFilter
     if (global) {
       const real = await realpath(this.path, this[_rpcache], this[_stcache])
       const newNodeOrLink = this.path === real ? _newNode : _newLink
@@ -132,8 +139,8 @@ module.exports = cls => class ActualLoader extends cls {
     await this[_loadFSTree](this.actualTree)
     this[_findFSParents]()
     this[_transplant](root)
-    // only reset the flags if we're not re-rooting, otherwise leave as-is
-    calcDepFlags(this.actualTree, root === null)
+    // only reset root flags if we're not re-rooting, otherwise leave as-is
+    calcDepFlags(this.actualTree, !root)
     return this.actualTree
   }
 
@@ -148,7 +155,8 @@ module.exports = cls => class ActualLoader extends cls {
       node.fsParent = root
     }
     for (const node of this.actualTree.children.values()) {
-      node.parent = root
+      if (this[_transplantFilter](node))
+        node.parent = root
     }
     this.actualTree = root
   }
diff --git a/test/arborist/load-actual.js b/test/arborist/load-actual.js
index a7a78fbde..deb6f257b 100644
--- a/test/arborist/load-actual.js
+++ b/test/arborist/load-actual.js
@@ -133,6 +133,29 @@ t.test('load a tree rooted on a different node', async t => {
 
   // should look the same, once we strip off the other/fixture paths
   t.equal(format(printTree(actual)), format(printTree(transp)), 'similar trees')
+
+  // now try with a transplant filter that keeps out the 'a' module
+  const rootFiltered = new Node({
+    meta: await Shrinkwrap.reset({path: other}),
+    path: other,
+    realpath: other,
+    pkg: require(path + '/package.json'),
+  })
+  rootFiltered.extraneous = false
+  rootFiltered.dev = false
+  rootFiltered.devOptional = false
+  rootFiltered.optional = false
+  rootFiltered.peer = false
+  const transpFilter = await new Arborist({path}).loadActual({
+    root: rootFiltered,
+    transplantFilter: n => n.name !== 'a'
+  })
+  t.equal(transpFilter.children.get('a'), undefined)
+  t.equal(transpFilter.children.get('b').path, resolve(other, 'node_modules/b'))
+  t.equal(transpFilter.children.get('c').path, resolve(other, 'node_modules/c'))
+  t.equal(transpFilter.children.get('a'), undefined)
+  t.equal(transpFilter.children.get('b').realpath, resolve(other, 'packages/b'))
+  t.equal(transpFilter.children.get('c').realpath, resolve(other, 'packages/c'))
 })
 
 t.test('looking outside of cwd', t => {