diff --git a/package.json b/package.json
index 020fd2f2e..3614b5f26 100644
--- a/package.json
+++ b/package.json
@@ -84,7 +84,12 @@
     "solarized-dark-syntax": "0.35.0",
     "solarized-light-syntax": "0.21.0",
     "archive-view": "0.57.0",
-    "autocomplete": "0.47.0",
+    "autocomplete-atom-api": "0.9.0",
+    "autocomplete-css": "0.7.2",
+    "autocomplete-emojis": "2.2.2",
+    "autocomplete-html": "0.7.1",
+    "autocomplete-plus": "2.15.1",
+    "autocomplete-snippets": "1.6.1",
     "autoflow": "0.23.0",
     "autosave": "0.20.0",
     "background-tips": "0.24.0",
diff --git a/spec/package-manager-spec.coffee b/spec/package-manager-spec.coffee
index 92dc21a13..1244ab984 100644
--- a/spec/package-manager-spec.coffee
+++ b/spec/package-manager-spec.coffee
@@ -824,3 +824,37 @@ describe "PackageManager", ->
           expect(atom.config.get('core.themes')).not.toContain packageName
           expect(atom.config.get('core.themes')).not.toContain packageName
           expect(atom.config.get('core.disabledPackages')).not.toContain packageName
+
+  describe "deleting non-bundled autocomplete packages", ->
+    [autocompleteCSSPath, autocompletePlusPath] = []
+    fs = require 'fs-plus'
+    path = require 'path'
+
+    beforeEach ->
+      fixturePath = path.resolve(__dirname, './fixtures/packages')
+      autocompleteCSSPath = path.join(fixturePath, 'autocomplete-css')
+      autocompletePlusPath = path.join(fixturePath, 'autocomplete-plus')
+
+      try
+        fs.mkdirSync(autocompleteCSSPath)
+        fs.writeFileSync(path.join(autocompleteCSSPath, 'package.json'), '{}')
+        fs.symlinkSync(path.join(fixturePath, 'package-with-main'), autocompletePlusPath, 'dir')
+
+      expect(fs.isDirectorySync(autocompleteCSSPath)).toBe true
+      expect(fs.isSymbolicLinkSync(autocompletePlusPath)).toBe true
+
+      jasmine.unspy(atom.packages, 'uninstallAutocompletePlus')
+
+    afterEach ->
+      try
+        fs.unlink autocompletePlusPath, ->
+
+    it "removes the packages", ->
+      atom.packages.loadPackages()
+
+      waitsFor ->
+        not fs.isDirectorySync(autocompleteCSSPath)
+
+      runs ->
+        expect(fs.isDirectorySync(autocompleteCSSPath)).toBe false
+        expect(fs.isSymbolicLinkSync(autocompletePlusPath)).toBe true
diff --git a/spec/spec-helper.coffee b/spec/spec-helper.coffee
index 0112042e2..2e4355a10 100644
--- a/spec/spec-helper.coffee
+++ b/spec/spec-helper.coffee
@@ -140,6 +140,8 @@ beforeEach ->
   spyOn(clipboard, 'writeText').andCallFake (text) -> clipboardContent = text
   spyOn(clipboard, 'readText').andCallFake -> clipboardContent
 
+  spyOn(atom.packages, 'uninstallAutocompletePlus')
+
   addCustomMatchers(this)
 
 afterEach ->
diff --git a/src/package-manager.coffee b/src/package-manager.coffee
index 8527188d3..606f72eda 100644
--- a/src/package-manager.coffee
+++ b/src/package-manager.coffee
@@ -303,6 +303,9 @@ class PackageManager
     # of the first package isn't skewed by being the first to require atom
     require '../exports/atom'
 
+    # TODO: remove after a few atom versions.
+    @uninstallAutocompletePlus()
+
     packagePaths = @getAvailablePackagePaths()
     packagePaths = packagePaths.filter (packagePath) => not @isPackageDisabled(path.basename(packagePath))
     packagePaths = _.uniq packagePaths, (packagePath) -> path.basename(packagePath)
@@ -409,6 +412,40 @@ class PackageManager
     message = "Failed to load the #{path.basename(packagePath)} package"
     atom.notifications.addError(message, {stack, detail, dismissable: true})
 
+  # TODO: remove these autocomplete-plus specific helpers after a few versions.
+  uninstallAutocompletePlus: ->
+    packageDir = null
+    devDir = path.join("dev", "packages")
+    for packageDirPath in @packageDirPaths
+      if not packageDirPath.endsWith(devDir)
+        packageDir = packageDirPath
+        break
+
+    if packageDir?
+      dirsToRemove = [
+        path.join(packageDir, 'autocomplete-plus')
+        path.join(packageDir, 'autocomplete-atom-api')
+        path.join(packageDir, 'autocomplete-css')
+        path.join(packageDir, 'autocomplete-html')
+        path.join(packageDir, 'autocomplete-emojis')
+        path.join(packageDir, 'autocomplete-snippets')
+      ]
+      for dirToRemove in dirsToRemove
+        @uninstallDirectory(dirToRemove)
+    return
+
+  uninstallDirectory: (directory) ->
+    symlinkPromise = new Promise (resolve) ->
+      fs.isSymbolicLink directory, (isSymLink) -> resolve(isSymLink)
+
+    dirPromise = new Promise (resolve) ->
+      fs.isDirectory directory, (isDir) -> resolve(isDir)
+
+    Promise.all([symlinkPromise, dirPromise]).then (values) ->
+      [isSymLink, isDir] = values
+      if not isSymLink and isDir
+        fs.remove directory, ->
+
 if Grim.includeDeprecatedAPIs
   EmitterMixin = require('emissary').Emitter
   EmitterMixin.includeInto(PackageManager)