diff --git a/packages/shrinkwrap/src/prune.ts b/packages/shrinkwrap/src/prune.ts
index a05a091308..fea785cbd1 100644
--- a/packages/shrinkwrap/src/prune.ts
+++ b/packages/shrinkwrap/src/prune.ts
@@ -72,7 +72,12 @@ export function prune (
   })
   if (importer.dependencies) {
     for (const dep of R.keys(importer.dependencies)) {
-      if (!shrDependencies[dep] && importer.dependencies[dep].startsWith('link:')) {
+      if (
+        !shrDependencies[dep] && importer.dependencies[dep].startsWith('link:') &&
+        // If the linked dependency was removed from package.json
+        // then it is removed from shrinkwrap.yaml as well
+        !(shrSpecs[dep] && !allDeps[dep])
+      ) {
         shrDependencies[dep] = importer.dependencies[dep]
       }
     }
diff --git a/packages/shrinkwrap/test/prune.ts b/packages/shrinkwrap/test/prune.ts
index 077cc08d61..df02cf3251 100644
--- a/packages/shrinkwrap/test/prune.ts
+++ b/packages/shrinkwrap/test/prune.ts
@@ -71,6 +71,38 @@ test('remove one redundant package', t => {
   t.end()
 })
 
+test('remove redundant linked package', t => {
+  t.deepEqual(prune({
+    shrinkwrapVersion: 3,
+    registry: 'https://registry.npmjs.org',
+    importers: {
+      '.': {
+        dependencies: {
+          'is-positive': 'link:../is-positive'
+        },
+        specifiers: {
+          'is-positive': '^1.0.0'
+        },
+      },
+    },
+    packages: {},
+  }, {
+    name: 'foo',
+    version: '1.0.0',
+    dependencies: {}
+  }, '.', DEFAULT_OPTS), {
+    shrinkwrapVersion: 3,
+    registry: 'https://registry.npmjs.org',
+    importers: {
+      '.': {
+        specifiers: {},
+      },
+    },
+  })
+
+  t.end()
+})
+
 test('keep all', t => {
   t.deepEqual(prune({
     shrinkwrapVersion: 3,
diff --git a/packages/supi/test/uninstall.ts b/packages/supi/test/uninstall.ts
index e57430fc38..5cf6487424 100644
--- a/packages/supi/test/uninstall.ts
+++ b/packages/supi/test/uninstall.ts
@@ -190,6 +190,7 @@ test('uninstalling a dependency from package that uses shared shrinkwrap', async
       version: '1.0.0',
       dependencies: {
         'is-positive': '1.0.0',
+        'project-2': '1.0.0',
       },
     },
     {
@@ -210,12 +211,28 @@ test('uninstalling a dependency from package that uses shared shrinkwrap', async
     },
   ]
 
-  await install(await testDefaults({ importers }))
+  await install(await testDefaults({
+    importers,
+    localPackages: {
+      'project-2': {
+        '1.0.0': {
+          directory: path.resolve('project-2'),
+          package: {
+            name: 'project-2',
+            version: '1.0.0',
+            dependencies: {
+              'is-negative': '1.0.0',
+            },
+          },
+        },
+      },
+    },
+  }))
 
   await projects['project-1'].has('is-positive')
   await projects['project-2'].has('is-negative')
 
-  await uninstall(['is-positive'], await testDefaults({
+  await uninstall(['is-positive', 'project-2'], await testDefaults({
     prefix: importers[0].prefix,
     shrinkwrapDirectory: process.cwd(),
   }))