diff --git a/src/index.ts b/src/index.ts
index e4c7da1..c240ee2 100644
--- a/src/index.ts
+++ b/src/index.ts
@@ -470,6 +470,26 @@ const parseArgv = (processArgv: string[]) => {
   return argv;
 };
 
+function validateCustomTemplateOptions(argv: Argv, templateName: string) {
+  const unsupportedOptions: string[] = [];
+  if (argv.tools !== undefined) {
+    unsupportedOptions.push('--tools');
+  }
+  if (argv.skill !== undefined) {
+    unsupportedOptions.push('--skill');
+  }
+  const templateVersion = argv.templateVersion ?? argv['template-version'];
+  if (templateVersion !== undefined) {
+    unsupportedOptions.push('--template-version');
+  }
+
+  if (unsupportedOptions.length) {
+    throw new Error(
+      `Template "${templateName}" does not support ${unsupportedOptions.join(', ')}. Remove the unsupported options and use the template's setup flow instead.`,
+    );
+  }
+}
+
 type ExtraTool = {
   /**
    * The value of the multiselect option.
@@ -846,6 +866,8 @@ export async function create({
       typeof template !== 'string' && template.name === templateName,
   );
   if (typeof customTemplate === 'object') {
+    validateCustomTemplateOptions(argv, templateName);
+
     await customTemplate.create({
       distFolder,
       packageName:
diff --git a/test/custom-templates.test.ts b/test/custom-templates.test.ts
index 614a11d..8c658c9 100644
--- a/test/custom-templates.test.ts
+++ b/test/custom-templates.test.ts
@@ -81,3 +81,19 @@ test('should propagate errors from a custom template', async () => {
 
   await expect(create(options)).rejects.toBe(error);
 });
+
+test.each([
+  {
+    args: ['--tools', '', '--skill', 'example-skill', '--template-version', ''],
+    unsupported: '--tools, --skill, --template-version',
+  },
+  { args: ['--templateVersion', '1.0.0'], unsupported: '--template-version' },
+])(
+  'should reject unsupported options: $args',
+  async ({ args, unsupported }) => {
+    await expect(
+      create({ ...options, argv: [...options.argv, ...args] }),
+    ).rejects.toThrow(`Template "external" does not support ${unsupported}.`);
+    expect(createTemplate).not.toHaveBeenCalled();
+  },
+);