diff --git a/src/adapter.js b/src/adapter.js
index 8d89ec6..e63d054 100644
--- a/src/adapter.js
+++ b/src/adapter.js
@@ -51,18 +51,20 @@
             System.bundles = [];
         }
 
-        var systemInstantiate = System.instantiate;
-        var http = location.protocol;
-        var slashes = http.concat('//');
-        var host = slashes.concat(window.location.host) + '/base/';
-        System.instantiate = function(load) {
-            var fileKey = load.name.replace(host, '');
-            if (karma.config.jspm.coverageFiles[fileKey]) {
-                var re = new RegExp('file://' + karma.config.jspm.basePath + '/','g');
-                load.source = karma.config.jspm.coverageFiles[fileKey].replace(re, host);
-            }
-            return systemInstantiate.call(System, load);
-        };
+        if (typeof karma.config.jspm.coverage === 'object') {
+            var systemInstantiate = System.instantiate;
+            var http = location.protocol;
+            var slashes = http.concat('//');
+            var host = slashes.concat(window.location.host) + '/base/';
+            System.instantiate = function(load) {
+                var fileKey = load.name.replace(host, '');
+                if (karma.config.jspm.coverage.files[fileKey]) {
+                    var re = new RegExp('file://' + karma.config.jspm.coverage.basePath + '/','g');
+                    load.source = karma.config.jspm.coverage.files[fileKey].replace(re, host);
+                }
+                return systemInstantiate.call(System, load);
+            };
+        }
 
         // Load everything specified in loadFiles in the specified order
         var promiseChain = Promise.resolve();
diff --git a/src/init.js b/src/init.js
index 233a29b..d208f19 100644
--- a/src/init.js
+++ b/src/init.js
@@ -102,13 +102,13 @@ module.exports = function(files, basePath, jspm, client, emitter) {
             return packagesPath + fileName + '.js';
         }
     }
-    
+
     Array.prototype.unshift.apply(files,
         configPaths.map(function(configPath) {
             return createPattern(configPath)
         })
     );
-    
+
     // Needed for JSPM 0.17 beta
     if(jspm.browser) {
         files.unshift(createPattern(browserPath));
@@ -139,7 +139,9 @@ module.exports = function(files, basePath, jspm, client, emitter) {
 
     // Allow Karma to serve all files within jspm_packages.
     // This allows jspm/SystemJS to load them
-    var jspmPattern = createServedPattern(packagesPath + '**/*', {nocache: jspm.cachePackages !== true});
+    var jspmPattern = createServedPattern(
+        packagesPath + '!(system-polyfills.src.js|system.src.js)/**', {nocache: jspm.cachePackages !== true}
+    );
     jspmPattern.watched = false;
     files.push(jspmPattern);
 };
diff --git a/src/preprocessor.js b/src/preprocessor.js
index 60df10d..2297901 100644
--- a/src/preprocessor.js
+++ b/src/preprocessor.js
@@ -27,14 +27,16 @@ function CoveragePreprocessor(basePath, client, reporters, helper, logger) {
     // create a jspm namespace to pass data to the browsers
     if (!client.jspm) client.jspm = {};
     // store instrumented sources to be executed by browser
-    client.jspm.coverageFiles = {};
+    client.jspm.coverage = {
+        files: {}
+    };
     // store basePath used to generate the key for each source in the obj above
-    client.jspm.basePath = basePath;
+    client.jspm.coverage.basePath = basePath;
     // temp folder to store instrumented files for sourcemap remapping
-    client.jspm.tempDirectory = path.join(__dirname, '../no-source-map/');
+    client.jspm.coverage.tempDirectory = path.join(__dirname, '../no-source-map/');
 
     // make temp directory
-    var tempDirectory = client.jspm.tempDirectory;
+    var tempDirectory = client.jspm.coverage.tempDirectory;
     if (!fs.existsSync(tempDirectory)) {
         fs.mkdirSync(tempDirectory);
     }
@@ -50,7 +52,7 @@ function CoveragePreprocessor(basePath, client, reporters, helper, logger) {
             // create a unique key to store the sources of modules for the browser
             var fileKey = getFileKey(getOSFilePath(load.address), basePath);
             // exclude the dependency modules (i.e. libraries) from instrumentation
-            if (client.jspm.coverageFiles[fileKey]) {
+            if (client.jspm.coverage.files[fileKey]) {
                 // put file's transpiled counterpart in temp folder
                 var filename;
                 var sourceMap = '';
@@ -87,7 +89,7 @@ function CoveragePreprocessor(basePath, client, reporters, helper, logger) {
                 }
 
                 // instrument with istanbul
-                client.jspm.coverageFiles[fileKey] = instrument.instrumentSync(
+                client.jspm.coverage.files[fileKey] = instrument.instrumentSync(
                     load.source,
                     // make the path-like file key into something that can be used as a name
                     filename
@@ -106,7 +108,7 @@ function CoveragePreprocessor(basePath, client, reporters, helper, logger) {
         // only files to be instrumented pass through here
         // store this information to allow "instantiate" to exclude
         // dependency modules (i.e. libraries)
-        client.jspm.coverageFiles[getFileKey(file.path, basePath)] = true;
+        client.jspm.coverage.files[getFileKey(file.path, basePath)] = true;
         // import modules
         systemJS.import(file.path).then(function () {
             done(content);
diff --git a/src/reporter.js b/src/reporter.js
index 738a09f..19dfe42 100644
--- a/src/reporter.js
+++ b/src/reporter.js
@@ -15,7 +15,7 @@ function CoverageReporter(rootConfig, helper, logger, emitter) {
     };
     config._onExit = function (done) {
         try {
-            rimraf.sync(rootConfig.client.jspm.tempDirectory);
+            rimraf.sync(rootConfig.client.jspm.coverage.tempDirectory);
         } catch(e) {
             log.error(e);
         }
diff --git a/test/testInit.spec.js b/test/testInit.spec.js
index a04f70c..2370a15 100644
--- a/test/testInit.spec.js
+++ b/test/testInit.spec.js
@@ -74,7 +74,7 @@ describe('jspm plugin init', function(){
     });
 
     it('should use the configured jspm_packages path and include it at the end of the files array', function(){
-        expect(normalPath(files[files.length - 1].pattern)).toEqual(normalPath(path.resolve(cwd, './custom_packages/**/*')));
+        expect(normalPath(files[files.length - 1].pattern)).toEqual(normalPath(path.resolve(cwd, './custom_packages/!(system-polyfills.src.js|system.src.js)/**')));
         expect(files[files.length - 1].included).toEqual(false);
         expect(files[files.length - 1].served).toEqual(true);
         expect(files[files.length - 1].watched).toEqual(false);