diff --git a/src/index.js b/src/index.js
index c1e2f151..9c7f5fa1 100644
--- a/src/index.js
+++ b/src/index.js
@@ -218,7 +218,7 @@ async function getInput({ entries, cwd, source, module }) {
 						(await jsOrTs(cwd, 'index')) ||
 						module,
 		)
-		.map(file => glob(file))
+		.map(file => glob(file, { cwd }))
 		.forEach(file => input.push(...file));
 
 	return input;
diff --git a/test/__snapshots__/index.test.js.snap b/test/__snapshots__/index.test.js.snap
index 27dedc37..fadc962b 100644
--- a/test/__snapshots__/index.test.js.snap
+++ b/test/__snapshots__/index.test.js.snap
@@ -1280,6 +1280,54 @@ exports[`fixtures build class-properties with microbundle 5`] = `
 "
 `;
 
+exports[`fixtures build cli-entry-with-cwd with microbundle 1`] = `
+"Used script: microbundle
+
+Directory tree:
+
+cli-entry
+  dist
+    cli-entry.esm.mjs
+    cli-entry.esm.mjs.map
+    cli-entry.js
+    cli-entry.js.map
+    cli-entry.umd.js
+    cli-entry.umd.js.map
+  package.json
+  src
+    one.js
+    two.js
+
+
+Build \\"cli-entry\\" to dist:
+187 B: cli-entry.js.gz
+138 B: cli-entry.js.br
+188 B: cli-entry.esm.mjs.gz
+139 B: cli-entry.esm.mjs.br
+272 B: cli-entry.umd.js.gz
+202 B: cli-entry.umd.js.br"
+`;
+
+exports[`fixtures build cli-entry-with-cwd with microbundle 2`] = `6`;
+
+exports[`fixtures build cli-entry-with-cwd with microbundle 3`] = `
+"var r=function(){try{var r=arguments;return Promise.resolve([].slice.call(r).reduce(function(r,e){return r+e},0))}catch(r){return Promise.reject(r)}};export default function(){try{var e=arguments,t=[].slice.call(e);return Promise.resolve(r.apply(void 0,t)).then(function(e){return Promise.resolve(r.apply(void 0,t)).then(function(r){return[e,r]})})}catch(r){return Promise.reject(r)}}
+//# sourceMappingURL=cli-entry.esm.mjs.map
+"
+`;
+
+exports[`fixtures build cli-entry-with-cwd with microbundle 4`] = `
+"var r=function(){try{var r=arguments;return Promise.resolve([].slice.call(r).reduce(function(r,e){return r+e},0))}catch(r){return Promise.reject(r)}};module.exports=function(){try{var e=arguments,t=[].slice.call(e);return Promise.resolve(r.apply(void 0,t)).then(function(e){return Promise.resolve(r.apply(void 0,t)).then(function(r){return[e,r]})})}catch(r){return Promise.reject(r)}};
+//# sourceMappingURL=cli-entry.js.map
+"
+`;
+
+exports[`fixtures build cli-entry-with-cwd with microbundle 5`] = `
+"!function(e,r){\\"object\\"==typeof exports&&\\"undefined\\"!=typeof module?module.exports=r():\\"function\\"==typeof define&&define.amd?define(r):(e||self).cliEntry=r()}(this,function(){var e=function(){try{var e=arguments;return Promise.resolve([].slice.call(e).reduce(function(e,r){return e+r},0))}catch(e){return Promise.reject(e)}};return function(){try{var r=arguments,n=[].slice.call(r);return Promise.resolve(e.apply(void 0,n)).then(function(r){return Promise.resolve(e.apply(void 0,n)).then(function(e){return[r,e]})})}catch(e){return Promise.reject(e)}}});
+//# sourceMappingURL=cli-entry.umd.js.map
+"
+`;
+
 exports[`fixtures build css-modules--false with microbundle 1`] = `
 "Used script: microbundle --no-sourcemap --css-modules false
 
diff --git a/test/fixtures/cli-entry-with-cwd/cli-entry/package.json b/test/fixtures/cli-entry-with-cwd/cli-entry/package.json
new file mode 100644
index 00000000..1a246559
--- /dev/null
+++ b/test/fixtures/cli-entry-with-cwd/cli-entry/package.json
@@ -0,0 +1,3 @@
+{
+  "name": "cli-entry"
+}
diff --git a/test/fixtures/cli-entry-with-cwd/cli-entry/src/one.js b/test/fixtures/cli-entry-with-cwd/cli-entry/src/one.js
new file mode 100644
index 00000000..c0a2efb0
--- /dev/null
+++ b/test/fixtures/cli-entry-with-cwd/cli-entry/src/one.js
@@ -0,0 +1,5 @@
+import { two } from './two';
+
+export default async function (...args) {
+	return [await two(...args), await two(...args)];
+}
diff --git a/test/fixtures/cli-entry-with-cwd/cli-entry/src/two.js b/test/fixtures/cli-entry-with-cwd/cli-entry/src/two.js
new file mode 100644
index 00000000..9f1f741b
--- /dev/null
+++ b/test/fixtures/cli-entry-with-cwd/cli-entry/src/two.js
@@ -0,0 +1,3 @@
+export async function two(...args) {
+	return args.reduce((total, value) => total + value, 0);
+}
diff --git a/test/fixtures/cli-entry-with-cwd/package.json b/test/fixtures/cli-entry-with-cwd/package.json
new file mode 100644
index 00000000..43901e3a
--- /dev/null
+++ b/test/fixtures/cli-entry-with-cwd/package.json
@@ -0,0 +1,6 @@
+{
+  "name": "cli-entry-with-cwd",
+  "scripts": {
+    "build": "microbundle src/one.js --cwd ./cli-entry"
+  }
+}
diff --git a/tools/build-fixture.js b/tools/build-fixture.js
index 653b63fa..82c35188 100644
--- a/tools/build-fixture.js
+++ b/tools/build-fixture.js
@@ -56,6 +56,10 @@ export const buildDirectory = async fixtureDir => {
 	await rimraf(resolve(`${fixturePath}/.rts2_cache_es`));
 	await rimraf(resolve(`${fixturePath}/.rts2_cache_umd`));
 
+	// Now that dirs have been cleared, reset the fixturePath back to the parent dir
+	if (fixtureDir.endsWith('-with-cwd')) {
+		fixturePath = resolve(FIXTURES_DIR, fixtureDir);
+	}
 	const script = await getBuildScript(fixturePath, DEFAULT_SCRIPT);
 
 	const prevDir = process.cwd();