diff --git a/lib/cli.js b/lib/cli.js
index a6875a6f1..bb8d1d715 100644
--- a/lib/cli.js
+++ b/lib/cli.js
@@ -72,7 +72,21 @@ exports.run = () => {
 			'update-snapshots',
 			'color'
 		],
-		default: Object.assign({color: true}, conf),
+		default: {
+			cache: conf.cache,
+			color: 'color' in conf ? conf.color : true,
+			concurrency: conf.concurrency,
+			failFast: conf.failFast,
+			init: conf.init,
+			match: conf.match,
+			powerAssert: conf.powerAssert,
+			serial: conf.serial,
+			tap: conf.tap,
+			timeout: conf.timeout,
+			updateSnapshots: conf.updateSnapshots,
+			verbose: conf.verbose,
+			watch: conf.watch
+		},
 		alias: {
 			t: 'tap',
 			v: 'verbose',
@@ -107,31 +121,34 @@ exports.run = () => {
 		throw new Error(colors.error(figures.cross) + ' The --require and -r flags are deprecated. Requirements should be configured in package.json - see documentation.');
 	}
 
+	// copy resultant cli.flags into conf for use with Api and elsewhere
+	Object.assign(conf, cli.flags);
+
 	const api = new Api({
-		failFast: cli.flags.failFast,
-		serial: cli.flags.serial,
+		failFast: conf.failFast,
+		serial: conf.serial,
 		require: arrify(conf.require),
-		cacheEnabled: cli.flags.cache !== false,
-		powerAssert: cli.flags.powerAssert !== false,
-		explicitTitles: cli.flags.watch,
-		match: arrify(cli.flags.match),
+		cacheEnabled: conf.cache !== false,
+		powerAssert: conf.powerAssert !== false,
+		explicitTitles: conf.watch,
+		match: arrify(conf.match),
 		babelConfig: babelConfigHelper.validate(conf.babel),
 		resolveTestsFrom: cli.input.length === 0 ? projectDir : process.cwd(),
 		projectDir,
-		timeout: cli.flags.timeout,
-		concurrency: cli.flags.concurrency ? parseInt(cli.flags.concurrency, 10) : 0,
-		updateSnapshots: cli.flags.updateSnapshots,
-		color: cli.flags.color
+		timeout: conf.timeout,
+		concurrency: conf.concurrency ? parseInt(conf.concurrency, 10) : 0,
+		updateSnapshots: conf.updateSnapshots,
+		color: conf.color
 	});
 
 	let reporter;
 
-	if (cli.flags.tap && !cli.flags.watch) {
+	if (conf.tap && !conf.watch) {
 		reporter = new TapReporter();
-	} else if (cli.flags.verbose || isCi) {
-		reporter = new VerboseReporter({color: cli.flags.color});
+	} else if (conf.verbose || isCi) {
+		reporter = new VerboseReporter({color: conf.color});
 	} else {
-		reporter = new MiniReporter({color: cli.flags.color, watching: cli.flags.watch});
+		reporter = new MiniReporter({color: conf.color, watching: conf.watch});
 	}
 
 	reporter.api = api;
@@ -150,7 +167,7 @@ exports.run = () => {
 
 	const files = cli.input.length ? cli.input : arrify(conf.files);
 
-	if (cli.flags.watch) {
+	if (conf.watch) {
 		try {
 			const watcher = new Watcher(logger, api, files, arrify(conf.source));
 			watcher.observeStdin(process.stdin);