diff --git a/scripts/dev-bundle-server-package.js b/scripts/dev-bundle-server-package.js
index 4a13da2523c..a10dfe61fd0 100644
--- a/scripts/dev-bundle-server-package.js
+++ b/scripts/dev-bundle-server-package.js
@@ -19,6 +19,9 @@ var packageJson = {
   name: "meteor-dev-bundle",
   // Version is not important but is needed to prevent warnings.
   version: "0.0.0",
+  scripts: {
+    install: "node npm-rebuild.js"
+  },
   dependencies: {
     fibers: fibersVersion,
     "meteor-promise": "0.5.1",
diff --git a/tools/isobuild/bundler.js b/tools/isobuild/bundler.js
index 7c3bca8b7a1..add1b6fe00f 100644
--- a/tools/isobuild/bundler.js
+++ b/tools/isobuild/bundler.js
@@ -1817,8 +1817,8 @@ class JsImage {
       load.push(loadItem);
     });
 
-    const setupScriptPieces = [];
     const rebuildDirs = Object.create(null);
+
     // node_modules resources from the packages. Due to appropriate
     // builder configuration, 'meteor bundle' and 'meteor deploy' copy
     // them, and 'meteor run' symlinks them. If these contain
@@ -1842,18 +1842,15 @@ class JsImage {
       }
     });
 
-    _.each(rebuildDirs, dir => {
-      setupScriptPieces.push("(cd ", dir, " && npm rebuild)\n");
+    // This JSON file will be read by npm-rebuild.js, which is executed to
+    // trigger rebuilds for all non-portable npm packages.
+    builder.write("npm-rebuilds.json", {
+      data: new Buffer(
+        JSON.stringify(Object.keys(rebuildDirs), null, 2) + "\n",
+        "utf8"
+      )
     });
 
-    if (setupScriptPieces.length) {
-      setupScriptPieces.unshift('#!/usr/bin/env bash\n', 'set -e\n\n');
-      builder.write('setup.sh', {
-        data: new Buffer(setupScriptPieces.join(''), 'utf8'),
-        executable: true
-      });
-    }
-
     // Control file
     builder.writeJson('program.json', {
       format: "javascript-image-pre1",
@@ -2062,6 +2059,7 @@ class ServerTarget extends JsImageTarget {
       "server-json.js",
       "mini-files.js",
       "npm-require.js",
+      "npm-rebuild.js",
     ], function (filename) {
       builder.write(filename, {
         file: files.pathJoin(
diff --git a/tools/static-assets/server/npm-rebuild.js b/tools/static-assets/server/npm-rebuild.js
new file mode 100644
index 00000000000..415ab9e32df
--- /dev/null
+++ b/tools/static-assets/server/npm-rebuild.js
@@ -0,0 +1,47 @@
+var path = require("path");
+var spawn = require("child_process").spawn;
+
+try {
+  // This JSON file gets written in meteor/tools/isobuild/bundler.js.
+  var rebuilds = require("./npm-rebuilds.json");
+} catch (e) {
+  if (e.code !== "MODULE_NOT_FOUND") {
+    throw e;
+  }
+  // If npm-rebuilds.json was not written, assume there is nothing that
+  // needs to be rebuilt.
+}
+
+// Make sure the npm finds this exact version of node in its $PATH.
+var PATH = path.dirname(process.execPath) + ":" + process.env.PATH;
+var env = Object.create(process.env, {
+  PATH: { value: PATH }
+});
+
+function rebuild(i) {
+  var dir = rebuilds && rebuilds[i];
+
+  if (! dir) {
+    // Print Node/V8/etc. versions for diagnostic purposes.
+    spawn("npm", ["version", "--json"], {
+      stdio: "inherit",
+      env: env
+    });
+
+    return;
+  }
+
+  spawn("npm", ["rebuild"], {
+    cwd: path.join(__dirname, dir),
+    stdio: "inherit",
+    env: env
+  }).on("exit", function (code) {
+    if (code !== 0) {
+      process.exit(code);
+    } else {
+      rebuild(i + 1);
+    }
+  });
+}
+
+rebuild(0);