If QuickBooks payroll direct deposit is not working, start by verifying employee bank account information for accuracy. Ensure there are sufficient funds in your business account to cover payroll. Check the status of your payroll service in QuickBooks under Help > About QuickBooks. Update your software to the latest version via Help > Update QuickBooks. Review payroll settings in Preferences to ensure everything is set correctly. If issues persist, contact your bank or QuickBooks support for further assistance.