diff --git a/doc/cli/npm-dedupe.md b/doc/cli/npm-dedupe.md
index d68832145f0a5..f193660da5630 100644
--- a/doc/cli/npm-dedupe.md
+++ b/doc/cli/npm-dedupe.md
@@ -43,10 +43,10 @@ be deleted.
 
 Arguments are ignored. Dedupe always acts on the entire tree.
 
-Modules
+### Modules
 
-Note that this operation transforms the dependency tree, but will never
-result in new modules being installed.
+Note that this operation automatically fixes broken installs, which can sometimes
+cause the installation of new packages, just like `npm-install(1)` does.
 
 ## SEE ALSO
 
diff --git a/lib/dedupe.js b/lib/dedupe.js
index 325faeaabcd43..9ed17f0f6b988 100644
--- a/lib/dedupe.js
+++ b/lib/dedupe.js
@@ -59,6 +59,10 @@ Deduper.prototype.loadIdealTree = function (cb) {
     [this, this.cloneCurrentTreeToIdealTree],
     [this, this.finishTracker, 'cloneCurrentTree'],
 
+    [this.newTracker(this.progress.loadIdealTree, 'loadIdealTree:loadShrinkwrap')],
+    [this, this.loadShrinkwrap],
+    [this, this.finishTracker, 'loadIdealTree:loadShrinkwrap'],
+
     [this.newTracker(this.progress.loadIdealTree, 'loadAllDepsIntoIdealTree', 10)],
     [ function (next) {
       loadExtraneous(self.idealTree, self.progress.loadAllDepsIntoIdealTree, next)
diff --git a/test/tap/dedupe-optional.js b/test/tap/dedupe-optional.js
new file mode 100644
index 0000000000000..a4a7a4fe72f26
--- /dev/null
+++ b/test/tap/dedupe-optional.js
@@ -0,0 +1,95 @@
+'use strict'
+const fs = require('fs')
+const path = require('path')
+const test = require('tap').test
+const mr = require('npm-registry-mock')
+const Tacks = require('tacks')
+const File = Tacks.File
+const Dir = Tacks.Dir
+const common = require('../common-tap.js')
+
+const basedir = path.join(__dirname, path.basename(__filename, '.js'))
+const testdir = path.join(basedir, 'testdir')
+const cachedir = path.join(basedir, 'cache')
+const globaldir = path.join(basedir, 'global')
+const tmpdir = path.join(basedir, 'tmp')
+
+const conf = {
+  cwd: testdir,
+  env: Object.assign({}, process.env, {
+    npm_config_cache: cachedir,
+    npm_config_tmp: tmpdir,
+    npm_config_prefix: globaldir,
+    npm_config_registry: common.registry,
+    npm_config_loglevel: 'warn'
+  })
+}
+
+let server
+const fixture = new Tacks(Dir({
+  cache: Dir(),
+  global: Dir(),
+  tmp: Dir(),
+  testdir: Dir({
+    'package-lock.json': File({
+      name: 'dedupe-optional',
+      version: '1.0.0',
+      lockfileVersion: 1,
+      requires: true,
+      dependencies: {
+        async: {
+          version: '0.9.2',
+          resolved: 'https://registry.npmjs.org/async/-/async-0.9.2.tgz',
+          integrity: 'sha1-rqdNXmHB+JlhO/ZL2mbUx48v0X0=',
+          optional: true
+        }
+      }
+    }),
+    'package.json': File({
+      name: 'dedupe-optional',
+      version: '1.0.0',
+      optionalDependencies: {
+        async: '*'
+      }
+    })
+  })
+}))
+
+test('setup', function (t) {
+  setup()
+  mr({port: common.port, throwOnUnmatched: true}, function (err, s) {
+    if (err) throw err
+    server = s
+    t.done()
+  })
+})
+
+test('dedupe keeps uninstalled packages in package-lock.json', function (t) {
+  t.comment('test for https://npm.community/t/3807')
+  common.npm(['dedupe'], conf, function (err, code) {
+    if (err) throw err
+    t.is(code, 0, 'command ran ok')
+
+    const shrinkwrap = JSON.parse(
+      fs.readFileSync(
+        path.join(testdir, 'package-lock.json'), 'utf8'))
+
+    t.ok(shrinkwrap.dependencies, 'npm dedupe kept packages')
+    t.done()
+  })
+})
+
+test('cleanup', function (t) {
+  server.close()
+  cleanup()
+  t.done()
+})
+
+function cleanup () {
+  fixture.remove(basedir)
+}
+
+function setup () {
+  cleanup()
+  fixture.create(basedir)
+}