diff --git a/src/io.ts b/src/io.ts
index 7a94f83af2..c9ddd26a5a 100644
--- a/src/io.ts
+++ b/src/io.ts
@@ -99,7 +99,7 @@ export function save (pkgPath: string, shrinkwrap: Shrinkwrap) {
   const privateShrinkwrapPath = path.join(pkgPath, PRIVATE_SHRINKWRAP_FILENAME)
 
   // empty shrinkwrap is not saved
-  if (Object.keys(shrinkwrap.dependencies).length === 0) {
+  if (Object.keys(shrinkwrap.specifiers).length === 0) {
     return Promise.all([
       rimraf(shrinkwrapPath),
       rimraf(privateShrinkwrapPath),
diff --git a/src/prune.ts b/src/prune.ts
index d2a7b4a99c..68d7290ae2 100644
--- a/src/prune.ts
+++ b/src/prune.ts
@@ -15,25 +15,6 @@ export default function prune (shr: Shrinkwrap, pkg: Package): Shrinkwrap {
   const dependencies = R.difference(R.keys(pkg.dependencies), optionalDependencies)
   const devDependencies = R.difference(R.difference(R.keys(pkg.devDependencies), optionalDependencies), dependencies)
 
-  if (shr.optionalDependencies) {
-    let optionalPkgIds: string[] = R.keys(shr.optionalDependencies)
-      .map((pkgName: string) => getPkgShortId(shr!.optionalDependencies![pkgName], pkgName))
-    copyDependencySubTree(packages, optionalPkgIds, shr, [], {registry: shr.registry, optional: true})
-  }
-
-  if (shr.devDependencies) {
-    let devPkgIds: string[] = R.keys(shr.devDependencies)
-      .map((pkgName: string) => getPkgShortId(shr!.devDependencies![pkgName], pkgName))
-    copyDependencySubTree(packages, devPkgIds, shr, [], {registry: shr.registry, dev: true})
-  }
-
-  let pkgIds: string[] = dependencies
-    .map((pkgName: string) => getPkgShortId(shr.dependencies[pkgName], pkgName))
-
-  copyDependencySubTree(packages, pkgIds, shr, [], {
-    registry: shr.registry,
-  })
-
   const allDeps = R.reduce(R.union, [], [optionalDependencies, devDependencies, dependencies])
   const specifiers: ResolvedDependencies = {}
   const shrDependencies: ResolvedDependencies = {}
@@ -52,6 +33,25 @@ export default function prune (shr: Shrinkwrap, pkg: Package): Shrinkwrap {
     }
   })
 
+  if (shrOptionalDependencies) {
+    let optionalPkgIds: string[] = R.keys(shrOptionalDependencies)
+      .map((pkgName: string) => getPkgShortId(shrOptionalDependencies[pkgName], pkgName))
+    copyDependencySubTree(packages, optionalPkgIds, shr, [], {registry: shr.registry, optional: true})
+  }
+
+  if (shrDevDependencies) {
+    let devPkgIds: string[] = R.keys(shrDevDependencies)
+      .map((pkgName: string) => getPkgShortId(shrDevDependencies[pkgName], pkgName))
+    copyDependencySubTree(packages, devPkgIds, shr, [], {registry: shr.registry, dev: true})
+  }
+
+  let pkgIds: string[] = dependencies
+    .map((pkgName: string) => getPkgShortId(shrDependencies[pkgName], pkgName))
+
+  copyDependencySubTree(packages, pkgIds, shr, [], {
+    registry: shr.registry,
+  })
+
   const result = {
     version: SHRINKWRAP_VERSION,
     specifiers,
@@ -70,28 +70,6 @@ export default function prune (shr: Shrinkwrap, pkg: Package): Shrinkwrap {
   return result
 }
 
-function copyDependencyTree (
-  resolvedPackages: ResolvedPackages,
-  shr: Shrinkwrap,
-  opts: {
-    registry: string,
-    dependencies: string[],
-    dev?: boolean,
-    optional?: boolean,
-  }
-) {
-  let pkgIds: string[] = opts.dependencies
-    .map((pkgName: string) => getPkgShortId(shr.dependencies[pkgName], pkgName))
-
-  copyDependencySubTree(resolvedPackages, pkgIds, shr, [], opts)
-
-  if (shr.optionalDependencies) {
-    let optionalPkgIds: string[] = R.keys(shr.optionalDependencies)
-      .map((pkgName: string) => getPkgShortId(shr!.optionalDependencies![pkgName], pkgName))
-    copyDependencySubTree(resolvedPackages, optionalPkgIds, shr, [], Object.assign({}, opts, {optional: true}))
-  }
-}
-
 function copyDependencySubTree (
   resolvedPackages: ResolvedPackages,
   pkgIds: string[],
diff --git a/test/prune.ts b/test/prune.ts
index 3334192e72..f396952aae 100644
--- a/test/prune.ts
+++ b/test/prune.ts
@@ -398,3 +398,52 @@ test('dev dependency should not have dev = true if it is used not only as dev',
 
   t.end()
 })
+
+test('remove dependencies that are not in the package', t => {
+  t.deepEqual(prune({
+    version: 3,
+    registry: 'https://registry.npmjs.org',
+    dependencies: {
+      'is-positive': '1.0.0'
+    },
+    devDependencies: {
+      'is-negative': '1.0.0'
+    },
+    optionalDependencies: {
+      'fsevents': '1.0.0'
+    },
+    specifiers: {
+      'is-positive': '^1.0.0',
+      'is-negative': '^1.0.0',
+      'fsevents': '^1.0.0',
+    },
+    packages: {
+      '/is-positive/1.0.0': {
+        resolution: {
+          integrity: 'sha1-ChbBDewTLAqLCzb793Fo5VDvg/g='
+        }
+      },
+      '/is-negative/1.0.0': {
+        resolution: {
+          integrity: 'sha1-ChbBDewTLAqLCzb793Fo5VDvg/g='
+        }
+      },
+      '/fsevents/1.0.0': {
+        resolution: {
+          integrity: 'sha1-ChbBDewTLAqLCzb793Fo5VDvg/g='
+        }
+      },
+    }
+  }, {
+    name: 'foo',
+    version: '1.0.0',
+  }), {
+    version: 3,
+    registry: 'https://registry.npmjs.org',
+    dependencies: {},
+    specifiers: {},
+    packages: {}
+  })
+
+  t.end()
+})