diff --git a/test/lib/commands/install.js b/test/lib/commands/install.js
index 632ca22be9e71..3bac44b1b0ba8 100644
--- a/test/lib/commands/install.js
+++ b/test/lib/commands/install.js
@@ -1,4 +1,6 @@
 const t = require('tap')
+const { join } = require('path')
+const { rmSync } = require('fs')
 
 const { load: _loadMockNpm } = require('../../fixtures/mock-npm')
 
@@ -327,3 +329,37 @@ t.test('completion', async t => {
     t.strictSame(res, [])
   })
 })
+
+t.test('workspace', async it => {
+  const cwd = process.cwd()
+
+  t.afterEach(() => {
+    process.chdir(cwd)
+  })
+
+  t.test('remove non-exist workspace node and its dependency', async t => {
+    const localPrefix = join(t.testdir(), 'prefix')
+    const { npm } = await loadMockNpm(t)
+
+    process.chdir(localPrefix)
+    // init and install root package and its workspaces
+    npm.config.set('yes', true)
+    await npm.exec('init', [])
+    npm.config.set('workspace', ['packages/a', 'packages/b'])
+    await npm.exec('init', [])
+    await npm.exec('install', [])
+
+    // remove one workspace node and reinstall
+    rmSync(join(localPrefix, 'packages/b'), { recursive: true, force: true })
+    await npm.exec('install', [])
+    const lockJson = require(join(localPrefix, 'package-lock.json'))
+
+    t.strictSame(lockJson.packages[''].workspaces, ['packages/a'], 'remove non-exist ws node')
+    t.equal(lockJson.packages['packages/b'], undefined, 'remove non-exist ws package')
+    t.equal(lockJson.packages['node_modules/b'],
+      undefined,
+      'remove non-exist ws node_modules package'
+    )
+    t.equal(lockJson.dependencies.b, undefined, 'remove non-exist ws dependency')
+  })
+})
diff --git a/workspaces/arborist/lib/shrinkwrap.js b/workspaces/arborist/lib/shrinkwrap.js
index d5448bbcba927..cb382b0ce456f 100644
--- a/workspaces/arborist/lib/shrinkwrap.js
+++ b/workspaces/arborist/lib/shrinkwrap.js
@@ -922,7 +922,18 @@ class Shrinkwrap {
         if (node === this.tree || node.isRoot || node.location === '') {
           continue
         }
+
         const loc = relpath(this.path, node.path)
+
+        // extraneous ws node should not commit
+        if (node.extraneous && root.workspaces && root.workspaces.length) {
+          const wsIndex = root.workspaces.findIndex(ws => ws === loc)
+          if (wsIndex > -1) {
+            root.workspaces.splice(wsIndex, 1)
+            continue
+          }
+        }
+
         this.data.packages[loc] = Shrinkwrap.metaFromNode(
           node,
           this.path,