diff --git a/lib/plugin.js b/lib/plugin.js
index faf18d9..8a5d9ff 100644
--- a/lib/plugin.js
+++ b/lib/plugin.js
@@ -13,7 +13,8 @@ module.exports = function (helper) {
             var root = helper.getRootPath(),
                 dstpath = path.resolve(root, options.destPath),
                 nodes = {},
-                nodesToRun = {};
+                nodesToRun = {},
+                sources = [];
 
             options || (options = {});
             options.sourceLevels || (options.sourceLevels = options.levels);
@@ -49,6 +50,8 @@ module.exports = function (helper) {
                                         (nodesToRun[node] = true);
                                     }
                                 }
+                            } else if (options.jsSuffixes.indexOf(file.suffix) !== -1) {
+                                sources.push(path.relative(root, file.fullname));
                             }
                         });
 
@@ -106,7 +109,7 @@ module.exports = function (helper) {
 
                 var toRun = Object.keys(nodesToRun);
 
-                return toRun.length && runner.run(toRun, root);
+                return toRun.length && runner.run(toRun, root, sources);
             });
         }
     };
diff --git a/lib/runner.js b/lib/runner.js
index e53bd54..6f9b148 100644
--- a/lib/runner.js
+++ b/lib/runner.js
@@ -11,11 +11,13 @@ var fs = require('fs'),
     covIdx;
 
 if (NEED_COVERAGE) {
-    covCollector = new (require('istanbul').Collector)();
+var istanbul = require('istanbul'),
+    covCollector = new (istanbul.Collector)(),
+    instrumenter = new (istanbul.Instrumenter)(),
     covIdx = 0;
 }
 
-exports.run = function (targets, root) {
+exports.run = function (targets, root, sources) {
     var isWinOS = path.sep === '\\',
         exec = require('child_process').exec,
         MOCHA_PHANTOM_BIN = path.resolve(__dirname, '../node_modules/.bin/mocha-phantomjs' + (isWinOS ? '.cmd' : '')),
@@ -126,11 +128,37 @@ exports.run = function (targets, root) {
         }
 
         function storeFinalCoverage() {
-            var covFile = path.resolve(root, 'coverage.json');
-
-            fs.writeFileSync(covFile, JSON.stringify(covCollector.getFinalCoverage()), 'utf8');
-
-            covCollector.dispose();
+            var covFile = path.resolve(root, 'coverage.json'),
+                store = covCollector.store,
+                transformer = instrumenter.instrumentSync.bind(instrumenter),
+                config = istanbul.config.loadFile(),
+                data = {};
+
+            // add all files not covered by specs with zero coverage
+            istanbul.matcherFor({
+                root: root,
+                includes: sources,
+                excludes: store.keys().concat(config.instrumentation.excludes())
+            }, function (err, matcher) {
+                matcher.files.forEach(function (file) {
+                    // As implemented here:
+                    // https://github.com/gotwarlost/istanbul/blob/master/lib/command/common/run-with-cover.js#L222
+                    var key = path.relative(root, file);
+                    transformer(fs.readFileSync(file, 'utf-8'), key);
+
+                    Object.keys(instrumenter.coverState.s).forEach(function (key) {
+                        instrumenter.coverState.s[key] = 0;
+                    });
+
+                    data[key] = instrumenter.coverState;
+                });
+
+                covCollector.add(data);
+
+                fs.writeFileSync(covFile, JSON.stringify(covCollector.getFinalCoverage()), 'utf8');
+
+                covCollector.dispose();
+            });
         }
 
         return deferer.promise();