diff --git a/src/cli.js b/src/cli.js
index 15f0b857..ea4984ba 100644
--- a/src/cli.js
+++ b/src/cli.js
@@ -12,7 +12,7 @@ import * as options from './utils/options';
 const commandMap = {
   ADD: { add: true },
   BIN: { bin: true },
-  CACHE: { cache: true },
+  BUILD: { build: true },
   CACHE_CLEAN: { clean: true },
   CACHE_DIR: { dir: true },
   CACHE_LIST: { list: true, ls: true },
@@ -103,7 +103,7 @@ function runCommandFromCli(args: options.Args, flags: options.Flags) {
     return commands.add(commands.toAddOptions(commandArgs, flags));
   } else if (commandMap.BIN[command]) {
     return commands.bin(commands.toBinOptions(commandArgs, flags));
-  } else if (commandMap.CACHE[command]) {
+  } else if (commandMap.BUILD[command]) {
     return commands.build(commands.toBuildOptions(commandArgs, flags));
   } else if (commandMap.CACHE_CLEAN[command]) {
     if (commandMap.CACHE_DIR[command]) {
diff --git a/src/commands/__tests__/build.test.js b/src/commands/__tests__/build.test.js
index a91bc68b..e7325487 100644
--- a/src/commands/__tests__/build.test.js
+++ b/src/commands/__tests__/build.test.js
@@ -1,4 +1,39 @@
 // @flow
 import { build, toBuildOptions } from '../build';
+import { copyFixtureIntoTempDir } from 'jest-fixtures';
+import * as boltRun from '../run';
 
-test('bolt build');
+jest.mock('../run');
+
+describe('bolt build', () => {
+  it('should call run with build script with no flags or arguments', async () => {
+    await build(toBuildOptions([], { '--': [] }));
+    expect(boltRun.run).toHaveBeenCalledWith({
+      cwd: undefined,
+      script: 'build',
+      scriptArgs: [],
+      scriptFlags: []
+    });
+  });
+
+  it('should call run with build script with flags and arguments', async () => {
+    await build(
+      toBuildOptions(['Babel'], {
+        compress: true,
+        target: 'Node8',
+        cwd: 'dummyPattern/dummyPath',
+        '--': []
+      })
+    );
+    expect(boltRun.run).toHaveBeenCalledWith({
+      cwd: 'dummyPattern/dummyPath',
+      script: 'build',
+      scriptArgs: ['Babel'],
+      scriptFlags: [
+        '--compress',
+        '--target=Node8',
+        '--cwd=dummyPattern/dummyPath'
+      ]
+    });
+  });
+});
diff --git a/src/commands/__tests__/check.test.js b/src/commands/__tests__/check.test.js
index 429168cf..f596d394 100644
--- a/src/commands/__tests__/check.test.js
+++ b/src/commands/__tests__/check.test.js
@@ -1,4 +1,39 @@
 // @flow
 import { check, toCheckOptions } from '../check';
+import { copyFixtureIntoTempDir } from 'jest-fixtures';
+import * as boltRun from '../run';
 
-test('bolt check');
+jest.mock('../run');
+
+describe('bolt check', () => {
+  it('should call run with build script with no flags or arguments', async () => {
+    await check(toCheckOptions([], { '--': [] }));
+    expect(boltRun.run).toHaveBeenCalledWith({
+      cwd: undefined,
+      script: 'check',
+      scriptArgs: [],
+      scriptFlags: []
+    });
+  });
+
+  it('should call run with build script with flags and arguments', async () => {
+    await check(
+      toCheckOptions(['Babel'], {
+        compress: true,
+        target: 'Node8',
+        cwd: 'dummyPattern/dummyPath',
+        '--': []
+      })
+    );
+    expect(boltRun.run).toHaveBeenCalledWith({
+      cwd: 'dummyPattern/dummyPath',
+      script: 'check',
+      scriptArgs: ['Babel'],
+      scriptFlags: [
+        '--compress',
+        '--target=Node8',
+        '--cwd=dummyPattern/dummyPath'
+      ]
+    });
+  });
+});
diff --git a/src/commands/__tests__/doc.test.js b/src/commands/__tests__/doc.test.js
index c9368d71..27c938fe 100644
--- a/src/commands/__tests__/doc.test.js
+++ b/src/commands/__tests__/doc.test.js
@@ -1,4 +1,39 @@
 // @flow
 import { doc, toDocOptions } from '../doc';
+import { copyFixtureIntoTempDir } from 'jest-fixtures';
+import * as boltRun from '../run';
 
-test('bolt doc');
+jest.mock('../run');
+
+describe('bolt doc', () => {
+  it('should call run with build script with no flags or arguments', async () => {
+    await doc(toDocOptions([], { '--': [] }));
+    expect(boltRun.run).toHaveBeenCalledWith({
+      cwd: undefined,
+      script: 'doc',
+      scriptArgs: [],
+      scriptFlags: []
+    });
+  });
+
+  it('should call run with build script with flags and arguments', async () => {
+    await doc(
+      toDocOptions(['Babel'], {
+        compress: true,
+        target: 'Node8',
+        cwd: 'dummyPattern/dummyPath',
+        '--': []
+      })
+    );
+    expect(boltRun.run).toHaveBeenCalledWith({
+      cwd: 'dummyPattern/dummyPath',
+      script: 'doc',
+      scriptArgs: ['Babel'],
+      scriptFlags: [
+        '--compress',
+        '--target=Node8',
+        '--cwd=dummyPattern/dummyPath'
+      ]
+    });
+  });
+});
diff --git a/src/commands/__tests__/format.test.js b/src/commands/__tests__/format.test.js
index 1f4bef63..89b662dd 100644
--- a/src/commands/__tests__/format.test.js
+++ b/src/commands/__tests__/format.test.js
@@ -1,4 +1,39 @@
 // @flow
 import { format, toFormatOptions } from '../format';
+import { copyFixtureIntoTempDir } from 'jest-fixtures';
+import * as boltRun from '../run';
 
-test('bolt format');
+jest.mock('../run');
+
+describe('bolt format', () => {
+  it('should call run with build script with no flags or arguments', async () => {
+    await format(toFormatOptions([], { '--': [] }));
+    expect(boltRun.run).toHaveBeenCalledWith({
+      cwd: undefined,
+      script: 'format',
+      scriptArgs: [],
+      scriptFlags: []
+    });
+  });
+
+  it('should call run with build script with flags and arguments', async () => {
+    await format(
+      toFormatOptions(['Babel'], {
+        compress: true,
+        target: 'Node8',
+        cwd: 'dummyPattern/dummyPath',
+        '--': []
+      })
+    );
+    expect(boltRun.run).toHaveBeenCalledWith({
+      cwd: 'dummyPattern/dummyPath',
+      script: 'format',
+      scriptArgs: ['Babel'],
+      scriptFlags: [
+        '--compress',
+        '--target=Node8',
+        '--cwd=dummyPattern/dummyPath'
+      ]
+    });
+  });
+});
diff --git a/src/commands/__tests__/lint.test.js b/src/commands/__tests__/lint.test.js
index 4aadae95..af832022 100644
--- a/src/commands/__tests__/lint.test.js
+++ b/src/commands/__tests__/lint.test.js
@@ -1,4 +1,39 @@
 // @flow
 import { lint, toLintOptions } from '../lint';
+import { copyFixtureIntoTempDir } from 'jest-fixtures';
+import * as boltRun from '../run';
 
-test('bolt lint');
+jest.mock('../run');
+
+describe('bolt lint', () => {
+  it('should call run with build script with no flags or arguments', async () => {
+    await lint(toLintOptions([], { '--': [] }));
+    expect(boltRun.run).toHaveBeenCalledWith({
+      cwd: undefined,
+      script: 'lint',
+      scriptArgs: [],
+      scriptFlags: []
+    });
+  });
+
+  it('should call run with build script with flags and arguments', async () => {
+    await lint(
+      toLintOptions(['Babel'], {
+        compress: true,
+        target: 'Node8',
+        cwd: 'dummyPattern/dummyPath',
+        '--': []
+      })
+    );
+    expect(boltRun.run).toHaveBeenCalledWith({
+      cwd: 'dummyPattern/dummyPath',
+      script: 'lint',
+      scriptArgs: ['Babel'],
+      scriptFlags: [
+        '--compress',
+        '--target=Node8',
+        '--cwd=dummyPattern/dummyPath'
+      ]
+    });
+  });
+});
diff --git a/src/commands/__tests__/test.test.js b/src/commands/__tests__/test.test.js
index 98ac850d..1e73b851 100644
--- a/src/commands/__tests__/test.test.js
+++ b/src/commands/__tests__/test.test.js
@@ -1,4 +1,39 @@
 // @flow
 import { test as test_, toTestOptions } from '../test';
+import { copyFixtureIntoTempDir } from 'jest-fixtures';
+import * as boltRun from '../run';
 
-test('bolt test');
+jest.mock('../run');
+
+describe('bolt lint', () => {
+  it('should call run with build script with no flags or arguments', async () => {
+    await test_(toTestOptions([], { '--': [] }));
+    expect(boltRun.run).toHaveBeenCalledWith({
+      cwd: undefined,
+      script: 'test',
+      scriptArgs: [],
+      scriptFlags: []
+    });
+  });
+
+  it('should call run with build script with flags and arguments', async () => {
+    await test_(
+      toTestOptions(['Babel'], {
+        compress: true,
+        target: 'Node8',
+        cwd: 'dummyPattern/dummyPath',
+        '--': []
+      })
+    );
+    expect(boltRun.run).toHaveBeenCalledWith({
+      cwd: 'dummyPattern/dummyPath',
+      script: 'test',
+      scriptArgs: ['Babel'],
+      scriptFlags: [
+        '--compress',
+        '--target=Node8',
+        '--cwd=dummyPattern/dummyPath'
+      ]
+    });
+  });
+});
diff --git a/src/commands/build.js b/src/commands/build.js
index 399b4d7f..c49fcf0a 100644
--- a/src/commands/build.js
+++ b/src/commands/build.js
@@ -5,7 +5,8 @@ import { run } from './run';
 
 export type BuildOptions = {|
   cwd?: string,
-  args: options.Args
+  args: options.Args,
+  scriptFlags: Array<string>
 |};
 
 export function toBuildOptions(
@@ -14,7 +15,8 @@ export function toBuildOptions(
 ): BuildOptions {
   return {
     cwd: options.string(flags.cwd, 'cwd'),
-    args: args
+    args: args,
+    scriptFlags: options.toScriptFlags(flags)
   };
 }
 
@@ -22,6 +24,7 @@ export async function build(opts: BuildOptions) {
   await run({
     cwd: opts.cwd,
     script: 'build',
-    scriptArgs: opts.args
+    scriptArgs: opts.args,
+    scriptFlags: opts.scriptFlags
   });
 }
diff --git a/src/commands/check.js b/src/commands/check.js
index c3f9edaa..f55030c7 100644
--- a/src/commands/check.js
+++ b/src/commands/check.js
@@ -5,7 +5,8 @@ import { run } from './run';
 
 export type CheckOptions = {|
   cwd?: string,
-  args: options.Args
+  args: options.Args,
+  scriptFlags: Array<string>
 |};
 
 export function toCheckOptions(
@@ -14,7 +15,8 @@ export function toCheckOptions(
 ): CheckOptions {
   return {
     cwd: options.string(flags.cwd, 'cwd'),
-    args: args
+    args: args,
+    scriptFlags: options.toScriptFlags(flags)
   };
 }
 
@@ -22,6 +24,7 @@ export async function check(opts: CheckOptions) {
   await run({
     cwd: opts.cwd,
     script: 'check',
-    scriptArgs: opts.args
+    scriptArgs: opts.args,
+    scriptFlags: opts.scriptFlags
   });
 }
diff --git a/src/commands/doc.js b/src/commands/doc.js
index 7dac4dfb..8cab5a61 100644
--- a/src/commands/doc.js
+++ b/src/commands/doc.js
@@ -5,7 +5,8 @@ import { run } from './run';
 
 export type DocOptions = {|
   cwd?: string,
-  args: options.Args
+  args: options.Args,
+  scriptFlags: Array<string>
 |};
 
 export function toDocOptions(
@@ -14,7 +15,8 @@ export function toDocOptions(
 ): DocOptions {
   return {
     cwd: options.string(flags.cwd, 'cwd'),
-    args: args
+    args: args,
+    scriptFlags: options.toScriptFlags(flags)
   };
 }
 
@@ -22,6 +24,7 @@ export async function doc(opts: DocOptions) {
   await run({
     cwd: opts.cwd,
     script: 'doc',
-    scriptArgs: opts.args
+    scriptArgs: opts.args,
+    scriptFlags: opts.scriptFlags
   });
 }
diff --git a/src/commands/format.js b/src/commands/format.js
index 17c2869a..a3487a92 100644
--- a/src/commands/format.js
+++ b/src/commands/format.js
@@ -5,7 +5,8 @@ import { run } from './run';
 
 export type FormatOptions = {|
   cwd?: string,
-  args: options.Args
+  args: options.Args,
+  scriptFlags: Array<string>
 |};
 
 export function toFormatOptions(
@@ -14,7 +15,8 @@ export function toFormatOptions(
 ): FormatOptions {
   return {
     cwd: options.string(flags.cwd, 'cwd'),
-    args: args
+    args: args,
+    scriptFlags: options.toScriptFlags(flags)
   };
 }
 
@@ -22,6 +24,7 @@ export async function format(opts: FormatOptions) {
   await run({
     cwd: opts.cwd,
     script: 'format',
-    scriptArgs: opts.args
+    scriptArgs: opts.args,
+    scriptFlags: opts.scriptFlags
   });
 }
diff --git a/src/commands/lint.js b/src/commands/lint.js
index 77f8a7bd..cfb4de29 100644
--- a/src/commands/lint.js
+++ b/src/commands/lint.js
@@ -5,7 +5,8 @@ import { run } from './run';
 
 export type LintOptions = {|
   cwd?: string,
-  args: options.Args
+  args: options.Args,
+  scriptFlags: Array<string>
 |};
 
 export function toLintOptions(
@@ -14,7 +15,8 @@ export function toLintOptions(
 ): LintOptions {
   return {
     cwd: options.string(flags.cwd, 'cwd'),
-    args: args
+    args: args,
+    scriptFlags: options.toScriptFlags(flags)
   };
 }
 
@@ -22,6 +24,7 @@ export async function lint(opts: LintOptions) {
   await run({
     cwd: opts.cwd,
     script: 'lint',
-    scriptArgs: opts.args
+    scriptArgs: opts.args,
+    scriptFlags: opts.scriptFlags
   });
 }
diff --git a/src/commands/run.js b/src/commands/run.js
index eab1f1f3..05466f71 100644
--- a/src/commands/run.js
+++ b/src/commands/run.js
@@ -8,7 +8,8 @@ import { BoltError } from '../utils/errors';
 export type RunOptions = {|
   cwd?: string,
   script: string,
-  scriptArgs: options.Args
+  scriptArgs: options.Args,
+  scriptFlags: Array<string>
 |};
 
 export function toRunOptions(
@@ -19,7 +20,8 @@ export function toRunOptions(
   return {
     cwd: options.string(flags.cwd, 'cwd'),
     script,
-    scriptArgs
+    scriptArgs,
+    scriptFlags: options.toScriptFlags(flags)
   };
 }
 
@@ -30,7 +32,7 @@ export async function run(opts: RunOptions) {
 
   if (script) {
     logger.cmd(script, opts.scriptArgs);
-    await yarn.run(pkg, opts.script, opts.scriptArgs);
+    await yarn.run(pkg, opts.script, opts.scriptArgs, opts.scriptFlags);
   } else {
     throw new BoltError(
       `Package at "${pkg.dir}" does not have a script named "${opts.script}"`
diff --git a/src/commands/test.js b/src/commands/test.js
index 871f158a..9a9e3b63 100644
--- a/src/commands/test.js
+++ b/src/commands/test.js
@@ -5,7 +5,8 @@ import { run } from './run';
 
 export type TestOptions = {|
   cwd?: string,
-  args: options.Args
+  args: options.Args,
+  scriptFlags: Array<string>
 |};
 
 export function toTestOptions(
@@ -14,7 +15,8 @@ export function toTestOptions(
 ): TestOptions {
   return {
     cwd: options.string(flags.cwd, 'cwd'),
-    args: args
+    args: args,
+    scriptFlags: options.toScriptFlags(flags)
   };
 }
 
@@ -22,6 +24,7 @@ export async function test(opts: TestOptions) {
   await run({
     cwd: opts.cwd,
     script: 'test',
-    scriptArgs: opts.args
+    scriptArgs: opts.args,
+    scriptFlags: opts.scriptFlags
   });
 }
diff --git a/src/utils/__tests__/options.test.js b/src/utils/__tests__/options.test.js
index d9931127..1898d636 100644
--- a/src/utils/__tests__/options.test.js
+++ b/src/utils/__tests__/options.test.js
@@ -4,4 +4,21 @@ import * as options from '../options';
 describe('options', () => {
   test('string');
   test('boolean');
+
+  describe('toScriptFlags', () => {
+    it('returns empty array if there were no custom flags passes', async () => {
+      const scriptFlags = await options.toScriptFlags({
+        '--': []
+      });
+      expect(scriptFlags).toEqual([]);
+    });
+    it('returns flags with value with the custom flags that are passed', async () => {
+      const scriptFlags = await options.toScriptFlags({
+        '--': [],
+        coverage: true,
+        target: 'Node9'
+      });
+      expect(scriptFlags).toEqual(['--coverage', '--target=Node9']);
+    });
+  });
 });
diff --git a/src/utils/options.js b/src/utils/options.js
index 832c4161..6e30702c 100644
--- a/src/utils/options.js
+++ b/src/utils/options.js
@@ -47,3 +47,18 @@ export function toDependency(dependencyString: string): Dependency {
   }
   return version ? { name, version } : { name };
 }
+
+export function toScriptFlags(flags: Flags) {
+  let scriptFlags = [];
+
+  Object.keys(flags).map(flag => {
+    if (flag === '--') return;
+    if (typeof flags[flag] === 'string') {
+      scriptFlags.push(`--${flag}=${flags[flag]}`);
+    } else {
+      scriptFlags.push(`--${flag}`);
+    }
+  });
+
+  return scriptFlags;
+}
diff --git a/src/utils/yarn.js b/src/utils/yarn.js
index bed551a7..0c600c37 100644
--- a/src/utils/yarn.js
+++ b/src/utils/yarn.js
@@ -53,7 +53,8 @@ export async function add(
 export async function run(
   pkg: Package,
   script: string,
-  args: Array<string> = []
+  args: Array<string> = [],
+  flags: Array<string> = []
 ) {
   const localYarn = path.join(await getLocalBinPath(), 'yarn');
   let spawnArgs = ['run', '-s', script];
@@ -62,6 +63,10 @@ export async function run(
     spawnArgs = spawnArgs.concat('--', args);
   }
 
+  if (flags.length) {
+    spawnArgs = spawnArgs.concat(flags);
+  }
+
   await processes.spawn(localYarn, spawnArgs, {
     cwd: pkg.dir,
     pkg: pkg,