diff --git a/README.md b/README.md
index dc8bb7390..778ad174d 100644
--- a/README.md
+++ b/README.md
@@ -60,6 +60,7 @@ to inline the source map in the transpiled code. For Babel that means setting
 the `sourceMaps` option to `inline`.
 
 ## Support For Custom File Extensions (.jsx, .es6)
+
 Supporting file extensions can be configured through either the configuration arguments or with the `nyc` config section in `package.json`.
 
 ```shell
@@ -148,11 +149,11 @@ As an alternative to providing a list of files to `exclude`, you can provide
 an `include` key to specify specific files that should be covered:
 
 ```json
-{"config": {
+{
   "nyc": {
     "include": ["**/build/umd/moment.js"]
   }
-}}
+}
 ```
 
 > Note: include defaults to `['**']`
@@ -175,6 +176,21 @@ You can run `nyc` with the optional `--cache` flag, to prevent it from
 instrumenting the same files multiple times. This can signficantly
 improve runtime performance.
 
+## Configuring nyc
+
+Any configuration options that can be set via the command line
+can also be specified in the `nyc` stanza of your package.json:
+
+```json
+{
+  "nyc": {
+    "lines": 99,
+    "check-coverage": false,
+    "report-dir": "./alternative"
+  },
+}
+```
+
 ## Configuring Istanbul
 
 Behind the scenes nyc uses [istanbul](https://www.npmjs.com/package/istanbul). You
diff --git a/bin/nyc.js b/bin/nyc.js
index 2ca50a1b1..966cb7bf0 100755
--- a/bin/nyc.js
+++ b/bin/nyc.js
@@ -14,56 +14,25 @@ var wrapper = require.resolve('./wrap.js')
 var yargs = require('yargs')
   .usage('$0 [command] [options]\n\nrun your tests with the nyc bin to instrument them with coverage')
   .command('report', 'run coverage report for .nyc_output', function (yargs) {
-    yargs
+    return yargs
       .usage('$0 report [options]')
-      .option('r', {
-        alias: 'reporter',
-        describe: 'coverage reporter(s) to use',
-        default: 'text'
-      })
-      .option('report-dir', {
-        describe: 'default directory to output coverage reports in',
-        default: 'coverage'
-      })
-      .help('h')
-      .alias('h', 'help')
       .example('$0 report --reporter=lcov', 'output an HTML lcov report to ./coverage')
   })
   .command('check-coverage', 'check whether coverage is within thresholds provided', function (yargs) {
-    yargs
+    return yargs
       .usage('$0 check-coverage [options]')
-      .option('b', {
-        alias: 'branches',
-        default: 0,
-        description: 'what % of branches must be covered?'
-      })
-      .option('f', {
-        alias: 'functions',
-        default: 0,
-        description: 'what % of functions must be covered?'
-      })
-      .option('l', {
-        alias: 'lines',
-        default: 90,
-        description: 'what % of lines must be covered?'
-      })
-      .option('s', {
-        alias: 'statements',
-        default: 0,
-        description: 'what % of statements must be covered?'
-      })
-      .help('h')
-      .alias('h', 'help')
       .example('$0 check-coverage --lines 95', "check whether the JSON in nyc's output folder meets the thresholds provided")
   })
   .option('r', {
     alias: 'reporter',
     describe: 'coverage reporter(s) to use',
-    default: 'text'
+    default: 'text',
+    global: true
   })
   .option('report-dir', {
     describe: 'default directory to output coverage reports in',
-    default: 'coverage'
+    default: 'coverage',
+    global: true
   })
   .option('s', {
     alias: 'silent',
@@ -100,27 +69,33 @@ var yargs = require('yargs')
   })
   .option('branches', {
     default: 0,
-    description: 'what % of branches must be covered?'
+    description: 'what % of branches must be covered?',
+    global: true
   })
   .option('functions', {
     default: 0,
-    description: 'what % of functions must be covered?'
+    description: 'what % of functions must be covered?',
+    global: true
   })
   .option('lines', {
     default: 90,
-    description: 'what % of lines must be covered?'
+    description: 'what % of lines must be covered?',
+    global: true
   })
   .option('statements', {
     default: 0,
-    description: 'what % of statements must be covered?'
+    description: 'what % of statements must be covered?',
+    global: true
   })
   .help('h')
   .alias('h', 'help')
-  .version(require('../package.json').version)
+  .version()
+  .pkgConf('nyc', process.cwd())
   .example('$0 npm test', 'instrument your tests with coverage')
   .example('$0 --require babel-core/polyfill --require babel-core/register npm test', 'instrument your tests with coverage and babel')
   .example('$0 report --reporter=text-lcov', 'output lcov report after running your tests')
   .epilog('visit http://git.io/vTJJB for list of available reporters')
+
 var argv = yargs.argv
 
 if (argv._[0] === 'report') {
diff --git a/index.js b/index.js
index 9b74903ca..456aeba6e 100755
--- a/index.js
+++ b/index.js
@@ -15,9 +15,9 @@ var SourceMapCache = require('./lib/source-map-cache')
 var convertSourceMap = require('convert-source-map')
 var md5hex = require('md5-hex')
 var findCacheDir = require('find-cache-dir')
-var pkgUp = require('pkg-up')
-var readPkg = require('read-pkg')
 var js = require('default-require-extensions/js')
+var pkgUp = require('pkg-up')
+var yargs = require('yargs')
 
 /* istanbul ignore next */
 if (/index\.covered\.js$/.test(__filename)) {
@@ -25,17 +25,15 @@ if (/index\.covered\.js$/.test(__filename)) {
 }
 
 function NYC (opts) {
-  opts = opts || {}
-
-  this._istanbul = opts.istanbul
-  this.subprocessBin = opts.subprocessBin || path.resolve(__dirname, './bin/nyc.js')
-  this._tempDirectory = opts.tempDirectory || './.nyc_output'
-  this._reportDir = opts.reportDir
+  var config = this._loadConfig(opts || {})
 
-  var config = this._loadConfig(opts)
+  this._istanbul = config.istanbul
+  this.subprocessBin = config.subprocessBin || path.resolve(__dirname, './bin/nyc.js')
+  this._tempDirectory = config.tempDirectory || './.nyc_output'
+  this._reportDir = config.reportDir
   this.cwd = config.cwd
 
-  this.reporter = arrify(opts.reporter || 'text')
+  this.reporter = arrify(config.reporter || 'text')
 
   // load exclude stanza from config.
   this.include = false
@@ -49,12 +47,12 @@ function NYC (opts) {
 
   this.cacheDirectory = findCacheDir({name: 'nyc', cwd: this.cwd})
 
-  this.enableCache = Boolean(this.cacheDirectory && (opts.enableCache === true || process.env.NYC_CACHE === 'enable'))
+  this.enableCache = Boolean(this.cacheDirectory && (config.enableCache === true || process.env.NYC_CACHE === 'enable'))
 
   // require extensions can be provided as config in package.json.
-  this.require = arrify(config.require || opts.require)
+  this.require = arrify(config.require)
 
-  this.extensions = arrify(config.extension || opts.extension).concat('.js').map(function (ext) {
+  this.extensions = arrify(config.extension).concat('.js').map(function (ext) {
     return ext.toLowerCase()
   })
 
@@ -73,18 +71,16 @@ NYC.prototype._loadConfig = function (opts) {
   var cwd = opts.cwd || process.env.NYC_CWD || process.cwd()
   var pkgPath = pkgUp.sync(cwd)
 
-  // you can specify config in the nyc stanza of package.json.
-  var config
   if (pkgPath) {
     cwd = path.dirname(pkgPath)
-    var pkg = readPkg.sync(pkgPath, {normalize: false})
-    config = pkg.nyc || (pkg.config && pkg.config.nyc)
   }
-  config = config || {}
 
-  config.cwd = cwd
+  opts.cwd = cwd
 
-  return config
+  return yargs([])
+    .pkgConf('nyc', cwd)
+    .default(opts)
+    .argv
 }
 
 NYC.prototype._createTransform = function (ext) {
diff --git a/package.json b/package.json
index 11f1a89b6..8e8d8390c 100644
--- a/package.json
+++ b/package.json
@@ -35,7 +35,9 @@
       "index.covered.js",
       "test/fixtures/_generateCoverage.js"
     ],
-    "extension": [".es6"]
+    "extension": [
+      ".es6"
+    ]
   },
   "standard": {
     "ignore": [
@@ -79,18 +81,18 @@
     "micromatch": "~2.1.6",
     "mkdirp": "^0.5.0",
     "pkg-up": "^1.0.0",
-    "read-pkg": "^1.1.0",
     "resolve-from": "^2.0.0",
     "rimraf": "^2.5.0",
     "signal-exit": "^2.1.1",
     "source-map": "^0.5.3",
     "spawn-wrap": "^1.1.1",
     "strip-bom": "^2.0.0",
-    "yargs": "^3.15.0"
+    "yargs": "^4.0.0"
   },
   "devDependencies": {
     "any-path": "^1.3.0",
     "chai": "^3.0.0",
+    "clear-require": "^1.0.1",
     "coveralls": "^2.11.4",
     "exists-sync": "0.0.3",
     "forking-tap": "^0.1.1",
diff --git a/test/fixtures/package.json b/test/fixtures/package.json
index c206db909..08a8051c5 100644
--- a/test/fixtures/package.json
+++ b/test/fixtures/package.json
@@ -7,13 +7,11 @@
     "nyc": "./bin/nyc.js",
     "nyc-report": "./bin/nyc-report.js"
   },
-  "config": {
-    "nyc": {
-      "exclude": [
-        "**/blarg",
-        "**/blerg"
-      ],
-      "extension": [".es6", ".foo.BAR"]
-    }
+  "nyc": {
+    "exclude": [
+      "**/blarg",
+      "**/blerg"
+    ],
+    "extension": [".es6", ".foo.BAR"]
   }
 }
diff --git a/test/src/nyc-test.js b/test/src/nyc-test.js
index 0ac7cf172..78a71ed6f 100644
--- a/test/src/nyc-test.js
+++ b/test/src/nyc-test.js
@@ -22,6 +22,7 @@ function NYC (opts) {
 }
 
 var path = require('path')
+var clearRequire = require('clear-require')
 var existsSync = require('exists-sync')
 var rimraf = require('rimraf')
 var sinon = require('sinon')
@@ -532,6 +533,7 @@ describe('nyc', function () {
         'test/nyc-test.js'
       ]
 
+      clearRequire('yargs')
       var yargv = require('yargs').argv
 
       var munged = (new NYC()).mungeArgs(yargv)