Does auto-pay automatically execute in Payment Runs?

Yes. When auto-pay is enabled and a valid payment method has been added, payments are automatically processed during Payment Runs.

When turning on auto-pay for customer with an outstanding balance; the next Payment Run will process the outstanding amount.

Learn more about the differences in Auto-Pay and Auto-Apply.

Note: If the failed payment auto-retry feature is enabled, see here to configure auto-pay settings when the maximum number of retry attempts has been reached.