diff --git a/lib/commands/check-coverage.js b/lib/commands/check-coverage.js
index c302ee916..8eb36eb50 100644
--- a/lib/commands/check-coverage.js
+++ b/lib/commands/check-coverage.js
@@ -13,6 +13,12 @@ exports.builder = function (yargs) {
       describe: 'a list of specific files and directories that should be excluded from coverage, glob patterns are supported, node_modules is always excluded',
       global: false
     })
+    .option('exclude-node-modules', {
+      default: true,
+      type: 'boolean',
+      describe: 'whether or not to exclude all node_module folders (i.e. **/node_modules/**) by default',
+      global: false
+    })
     .option('exclude-after-remap', {
       default: true,
       type: 'boolean',
diff --git a/lib/commands/instrument.js b/lib/commands/instrument.js
index 3c0fe9d3b..c22475c24 100644
--- a/lib/commands/instrument.js
+++ b/lib/commands/instrument.js
@@ -59,6 +59,12 @@ exports.builder = function (yargs) {
       default: testExclude.defaultExclude,
       describe: 'a list of specific files and directories that should not be instrumented, glob patterns are supported'
     })
+    .option('exclude-node-modules', {
+      default: true,
+      type: 'boolean',
+      describe: 'whether or not to exclude all node_module folders (i.e. **/node_modules/**) by default',
+      global: false
+    })
     .option('es-modules', {
       default: true,
       type: 'boolean',
@@ -100,20 +106,7 @@ exports.handler = function (argv) {
     ? './lib/instrumenters/istanbul'
     : './lib/instrumenters/noop'
 
-  const nyc = new NYC({
-    instrumenter: argv.instrumenter,
-    sourceMap: argv.sourceMap,
-    produceSourceMap: argv.produceSourceMap,
-    extension: argv.extension,
-    require: argv.require,
-    cwd: argv.cwd,
-    compact: argv.compact,
-    preserveComments: argv.preserveComments,
-    include: argv.include,
-    exclude: argv.exclude,
-    esModules: argv.esModules,
-    exitOnError: argv.exitOnError
-  })
+  const nyc = new NYC(argv)
 
   nyc.instrumentAllFiles(argv.input, argv.output, err => {
     if (err) {
diff --git a/lib/commands/report.js b/lib/commands/report.js
index 8dfc0f4ab..739ff30dc 100644
--- a/lib/commands/report.js
+++ b/lib/commands/report.js
@@ -30,6 +30,12 @@ exports.builder = function (yargs) {
       describe: 'a list of specific files and directories that should be excluded from coverage, glob patterns are supported, node_modules is always excluded',
       global: false
     })
+    .option('exclude-node-modules', {
+      default: true,
+      type: 'boolean',
+      describe: 'whether or not to exclude all node_module folders (i.e. **/node_modules/**) by default',
+      global: false
+    })
     .option('exclude-after-remap', {
       default: true,
       type: 'boolean',
diff --git a/test/fixtures/exclude-node-modules/.gitignore b/test/fixtures/exclude-node-modules/.gitignore
new file mode 100644
index 000000000..9ef48a5db
--- /dev/null
+++ b/test/fixtures/exclude-node-modules/.gitignore
@@ -0,0 +1,2 @@
+!node_modules
+node_modules/.cache/
diff --git a/test/fixtures/exclude-node-modules/bin/do-nothing.js b/test/fixtures/exclude-node-modules/bin/do-nothing.js
new file mode 100644
index 000000000..e69de29bb
diff --git a/test/fixtures/exclude-node-modules/node_modules/@istanbuljs/fake-module-1/index.js b/test/fixtures/exclude-node-modules/node_modules/@istanbuljs/fake-module-1/index.js
new file mode 100644
index 000000000..6be02374d
--- /dev/null
+++ b/test/fixtures/exclude-node-modules/node_modules/@istanbuljs/fake-module-1/index.js
@@ -0,0 +1 @@
+console.log('hello world');
diff --git a/test/fixtures/exclude-node-modules/node_modules/@istanbuljs/fake-module-2/index.js b/test/fixtures/exclude-node-modules/node_modules/@istanbuljs/fake-module-2/index.js
new file mode 100644
index 000000000..6be02374d
--- /dev/null
+++ b/test/fixtures/exclude-node-modules/node_modules/@istanbuljs/fake-module-2/index.js
@@ -0,0 +1 @@
+console.log('hello world');
diff --git a/test/fixtures/exclude-node-modules/package.json b/test/fixtures/exclude-node-modules/package.json
new file mode 100644
index 000000000..0967ef424
--- /dev/null
+++ b/test/fixtures/exclude-node-modules/package.json
@@ -0,0 +1 @@
+{}
diff --git a/test/nyc-integration.js b/test/nyc-integration.js
index 53527ffd8..88155a667 100644
--- a/test/nyc-integration.js
+++ b/test/nyc-integration.js
@@ -1737,6 +1737,138 @@ describe('the nyc cli', function () {
       })
     })
   })
+
+  describe('exclude-node-modules', () => {
+    const fixturesENM = path.resolve(__dirname, './fixtures/exclude-node-modules')
+    const globalArgs = [
+      bin,
+      '--all=true',
+      '--cache=false',
+      '--per-file=true',
+      '--exclude-node-modules=false',
+      '--include=node_modules/@istanbuljs/fake-module-1/**'
+    ]
+    const spawnOpts = {
+      cwd: fixturesENM,
+      env: env
+    }
+    const noCoverageError = `ERROR: Coverage for lines (0%) does not meet threshold (90%) for ${path.join(fixturesENM, 'node_modules/@istanbuljs/fake-module-1/index.js')}\n`
+
+    it('execute', done => {
+      function checkReport (code, stderr, stdout, next) {
+        code.should.equal(1)
+        stderr.should.equal(noCoverageError)
+        stdoutShouldEqual(stdout, `
+          ----------|----------|----------|----------|----------|-------------------|
+          File      |  % Stmts | % Branch |  % Funcs |  % Lines | Uncovered Line #s |
+          ----------|----------|----------|----------|----------|-------------------|
+          All files |        0 |      100 |      100 |        0 |                   |
+           index.js |        0 |      100 |      100 |        0 |                 1 |
+          ----------|----------|----------|----------|----------|-------------------|`)
+        next()
+      }
+
+      function executeMainCommand () {
+        const args = [
+          ...globalArgs,
+          '--check-coverage=true',
+          process.execPath, './bin/do-nothing.js'
+        ]
+
+        const proc = spawn(process.execPath, args, spawnOpts)
+
+        var stderr = ''
+        proc.stderr.on('data', function (chunk) {
+          stderr += chunk
+        })
+
+        var stdout = ''
+        proc.stdout.on('data', function (chunk) {
+          stdout += chunk
+        })
+
+        proc.on('close', code => checkReport(code, stderr, stdout, executeReport))
+      }
+
+      function executeReport () {
+        const args = [
+          ...globalArgs,
+          '--check-coverage=true',
+          'report'
+        ]
+
+        const proc = spawn(process.execPath, args, spawnOpts)
+
+        var stderr = ''
+        proc.stderr.on('data', function (chunk) {
+          stderr += chunk
+        })
+
+        var stdout = ''
+        proc.stdout.on('data', function (chunk) {
+          stdout += chunk
+        })
+
+        proc.on('close', code => checkReport(code, stderr, stdout, executeCheckCoverage))
+      }
+
+      function executeCheckCoverage () {
+        const args = [
+          ...globalArgs,
+          'check-coverage'
+        ]
+
+        const proc = spawn(process.execPath, args, spawnOpts)
+
+        var stderr = ''
+        proc.stderr.on('data', function (chunk) {
+          stderr += chunk
+        })
+
+        var stdout = ''
+        proc.stdout.on('data', function (chunk) {
+          stdout += chunk
+        })
+
+        proc.on('close', code => {
+          code.should.equal(1)
+          stderr.should.equal(noCoverageError)
+          stdoutShouldEqual(stdout, '')
+          done()
+        })
+      }
+
+      executeMainCommand()
+    })
+
+    it('instrument', done => {
+      const args = [
+        ...globalArgs,
+        'instrument',
+        'node_modules'
+      ]
+
+      const proc = spawn(process.execPath, args, spawnOpts)
+
+      var stderr = ''
+      proc.stderr.on('data', function (chunk) {
+        stderr += chunk
+      })
+
+      var stdout = ''
+      proc.stdout.on('data', function (chunk) {
+        stdout += chunk
+      })
+
+      proc.on('close', code => {
+        code.should.equal(0)
+        stderr.should.equal('')
+        stdout.should.match(/fake-module-1/)
+        stdout.should.not.match(/fake-module-2/)
+        done()
+      })
+    })
+  })
 })
 
 function stdoutShouldEqual (stdout, expected) {