It is now possible to pay your PAYE due via Direct Debit. The PAYE payment is due by the 22nd of the month following the tax month of the pay date, so a pay date of the 5th of May would be due by the 22nd of May for instance.
The PAYE payment to HMRC takes into account all the liabilities and credits, so the employee tax and National Insurance (NI) and the employer’s NI as well as any Employment Allowance, Statutory Maternity Pay recovery, Apprenticeship Levy etc. It is also worthwhile noting it is the year to date value that is critical, so the amount owed is the amount year to date less any payments already made.
If you want to pay HMRC via direct debit you apply via your Government Gateway and need to apply a couple of weeks prior to the first due date. The Direct Debit is currently collected on or just after the 22nd.
As of 19th April 2023 HMRC announce they still have issues with late payment notices going to employers with valid Direct Debits in place. HMRC hope to correct this in the near future.