diff --git a/lib/compiler.js b/lib/compiler.js
index 04f2845..e75ff6b 100644
--- a/lib/compiler.js
+++ b/lib/compiler.js
@@ -1,4 +1,5 @@
 var assert = require('assert');
+var cloneDeep = require('lodash.clonedeep');
 var fs = require('fs');
 var path = require('path');
 var toposort = require('toposort');
@@ -50,14 +51,17 @@ module.exports = function compile(options) {
   var modelInstructions = buildAllModelInstructions(
     modelsRootDir, modelsConfig, modelSources);
 
-  return {
+  // When executor passes the instruction to loopback methods,
+  // loopback modifies the data. Since we are loading the data using `require`,
+  // such change affects also code that calls `require` for the same file.
+  return cloneDeep({
     config: appConfig,
     dataSources: dataSourcesConfig,
     models: modelInstructions,
     files: {
       boot: bootScripts
     }
-  };
+  });
 };
 
 function assertIsValidConfig(name, config) {
diff --git a/package.json b/package.json
index 65c14ef..7a9002c 100644
--- a/package.json
+++ b/package.json
@@ -1,6 +1,6 @@
 {
   "name": "loopback-boot",
-  "version": "2.0.0-beta2",
+  "version": "2.0.0-beta3",
   "description": "Convention-based bootstrapper for LoopBack applications",
   "keywords": [
     "StrongLoop",
@@ -25,6 +25,7 @@
   "dependencies": {
     "commondir": "0.0.1",
     "debug": "^0.8.1",
+    "lodash.clonedeep": "^2.4.1",
     "semver": "^2.3.0",
     "toposort": "^0.2.10",
     "underscore": "^1.6.0"
diff --git a/test/compiler.test.js b/test/compiler.test.js
index e128235..5b6e450 100644
--- a/test/compiler.test.js
+++ b/test/compiler.test.js
@@ -402,6 +402,16 @@ describe('compiler', function() {
       expect(function() { boot.compile(appdir.PATH); })
         .to.throw(/cyclic dependency/i);
     });
+
+    it('returns a new copy of JSON data', function() {
+      appdir.createConfigFilesSync();
+
+      var instructions = boot.compile(appdir.PATH);
+      instructions.config.modified = true;
+
+      instructions = boot.compile(appdir.PATH);
+      expect(instructions.config).to.not.have.property('modified');
+    });
   });
 });