diff --git a/.changeset/checkout-flag-precedence.md b/.changeset/checkout-flag-precedence.md
new file mode 100644
index 000000000..bf0d34217
--- /dev/null
+++ b/.changeset/checkout-flag-precedence.md
@@ -0,0 +1,5 @@
+---
+'@openfn/cli': patch
+---
+
+An explicit `--checkout` or `--no-checkout` on `project deploy` now overrides `OPENFN_NO_CHECKOUT_AFTER_DEPLOY`
diff --git a/packages/cli/src/projects/options.ts b/packages/cli/src/projects/options.ts
index cf266a8d5..855a09431 100644
--- a/packages/cli/src/projects/options.ts
+++ b/packages/cli/src/projects/options.ts
@@ -65,13 +65,13 @@ export const checkout: CLIOption = {
   name: 'checkout',
   yargs: {
     boolean: true,
-    default: true,
     description:
       'Checkout the project after deploying. Use --no-checkout or OPENFN_NO_CHECKOUT_AFTER_DEPLOY=true to skip',
   },
   ensure: (opts: any) => {
-    if (process.env.OPENFN_NO_CHECKOUT_AFTER_DEPLOY === 'true') {
-      opts.checkout = false;
+    // An explicit --checkout or --no-checkout always beats the env var
+    if (opts.checkout === undefined) {
+      opts.checkout = process.env.OPENFN_NO_CHECKOUT_AFTER_DEPLOY !== 'true';
     }
   },
 };
diff --git a/packages/cli/test/projects/options.test.ts b/packages/cli/test/projects/options.test.ts
new file mode 100644
index 000000000..56025ce31
--- /dev/null
+++ b/packages/cli/test/projects/options.test.ts
@@ -0,0 +1,63 @@
+import test from 'ava';
+import yargs from 'yargs';
+
+import { command } from '../../src/projects/deploy';
+
+const ENV = 'OPENFN_NO_CHECKOUT_AFTER_DEPLOY';
+const original = process.env[ENV];
+
+test.afterEach.always(() => {
+  if (original === undefined) {
+    delete process.env[ENV];
+  } else {
+    process.env[ENV] = original;
+  }
+});
+
+// Parsing runs the command handler (ensure), so this returns the final options
+const parse = (cmd: string) =>
+  yargs()
+    .command(command as any)
+    .parse(cmd) as any;
+
+test.serial('checkout defaults to true', (t) => {
+  delete process.env[ENV];
+  const options = parse('deploy');
+  t.true(options.checkout);
+});
+
+test.serial('env=true with no flag skips checkout', (t) => {
+  process.env[ENV] = 'true';
+  const options = parse('deploy');
+  t.false(options.checkout);
+});
+
+test.serial('env=false with no flag checks out', (t) => {
+  process.env[ENV] = 'false';
+  const options = parse('deploy');
+  t.true(options.checkout);
+});
+
+test.serial('env=1 (truthy but not "true") with no flag checks out', (t) => {
+  process.env[ENV] = '1';
+  const options = parse('deploy');
+  t.true(options.checkout);
+});
+
+test.serial('env=true with --checkout checks out', (t) => {
+  process.env[ENV] = 'true';
+  const options = parse('deploy --checkout');
+  t.true(options.checkout);
+});
+
+test.serial('env=false with --no-checkout skips checkout', (t) => {
+  process.env[ENV] = 'false';
+  const options = parse('deploy --no-checkout');
+  t.false(options.checkout);
+});
+
+test.serial('env unset with --no-checkout skips checkout', (t) => {
+  delete process.env[ENV];
+  const options = parse('deploy --no-checkout');
+  t.false(options.checkout);
+});