diff --git a/.gitignore b/.gitignore
index b2b4cf15a..1d0275d10 100644
--- a/.gitignore
+++ b/.gitignore
@@ -12,4 +12,3 @@ debug.log
 docs/output
 docs/includes
 spec/fixtures/evil-files/
-/apm
diff --git a/.gitmodules b/.gitmodules
deleted file mode 100644
index e4335ef79..000000000
--- a/.gitmodules
+++ /dev/null
@@ -1,3 +0,0 @@
-[submodule "vendor/apm"]
-	path = vendor/apm
-	url = https://github.com/atom/apm.git
diff --git a/apm/README.md b/apm/README.md
new file mode 100644
index 000000000..0556f775f
--- /dev/null
+++ b/apm/README.md
@@ -0,0 +1 @@
+This folder is where APM is installed to so that it is bundled with Atom.
diff --git a/apm/package.json b/apm/package.json
new file mode 100644
index 000000000..9ff4f7e39
--- /dev/null
+++ b/apm/package.json
@@ -0,0 +1,11 @@
+{
+  "name": "atom-bundled-apm",
+  "description": "Atom's bundled APM",
+  "repository": {
+    "type": "git",
+    "url": "https://github.com/atom/atom.git"
+  },
+  "dependencies": {
+    "atom-package-manager": "0.41.0"
+  }
+}
diff --git a/script/bootstrap b/script/bootstrap
index 5fbd39981..4af047306 100755
--- a/script/bootstrap
+++ b/script/bootstrap
@@ -25,7 +25,6 @@ function executeCommands(commands, done, index) {
     done(null);
 }
 
-var apmVendorPath = path.resolve(__dirname, '..', 'vendor', 'apm');
 var apmInstallPath = path.resolve(__dirname, '..', 'apm');
 if (!fs.existsSync(apmInstallPath))
   fs.mkdirSync(apmInstallPath);
@@ -42,11 +41,8 @@ var packagesToDedupe = ['fs-plus', 'humanize-plus', 'oniguruma', 'roaster', 'sea
 var echoNewLine = process.platform == 'win32' ? 'echo.' : 'echo';
 
 var commands = [
-  'git submodule --quiet sync',
-  'git submodule --quiet update --recursive --init',
   {command: 'npm' + npmFlags + 'install --quiet', options: {cwd: path.resolve(__dirname, '..', 'build'), ignoreStdout: true}},
-  {command: npmPath + npmFlags + 'install --quiet', options: {cwd: apmVendorPath, ignoreStdout: true}},
-  {command: npmPath + npmFlags + 'install --quiet ' + apmVendorPath, options: {cwd: apmInstallPath, ignoreStdout: true}},
+  {command: npmPath + npmFlags + 'install --quiet', options: {cwd: apmInstallPath, ignoreStdout: true}},
   echoNewLine,
   apmPath + ' clean ' + apmFlags,
   apmPath + ' install --quiet ' + apmFlags,
diff --git a/script/clean b/script/clean
index 79f31d4b0..e55668215 100755
--- a/script/clean
+++ b/script/clean
@@ -18,7 +18,6 @@ var commands = [
   [__dirname, '..', 'node_modules'],
   [__dirname, '..', 'build', 'node_modules'],
   [__dirname, '..', 'apm', 'node_modules'],
-  [__dirname, '..', 'vendor', 'apm', 'node_modules'],
   [__dirname, '..', 'atom-shell'],
   [home, '.atom', '.node-gyp'],
   [home, '.atom', 'storage'],
diff --git a/vendor/apm b/vendor/apm
deleted file mode 160000
index d349e4526..000000000
--- a/vendor/apm
+++ /dev/null
@@ -1 +0,0 @@
-Subproject commit d349e4526388f8b5afc218beaa02ffeaf3a4f2e1