When doing bookkeeping, I am often asked if bank fees and card fees are subject to VAT. In my experience, different accountants and bookkeepers consider fees to either be Exempt of VAT or to not involve VAT at all ...
Exempt of VAT us assigned to 'T2' in Sage or 'Except Expenses' in Xero. If it is outside the scope of VAT then it is 'T9' in Sage and 'No VAT' in Xero. The difference with the two approaches is that with 'exempt', the net value appears in the total purchases box on the VAT return. With 'no VAT' there is nothing from the transaction reported on the VAT return.
In my own experiences with the VAT office, either approach seems acceptable as the numbers involved are usually very low. I advise my clients to pick the one which makes sense to them and just be consistent.
However, some of the other payment services may need researching a little more deeply, especially if the fee is seen to be as part of a financial service they provide, where the company is based, and where fees are due.
As of 1st September 2020, there was a change in the application of tax laws in France and the UK which meant GoCardless could no longer benefit from a VAT exemption which previously applied to the supply of payment services.
From that date forward their fees incur VAT. If you are a VAT registered business in the UK, it just means you can reclaim this VAT charge and it makes no difference to your bottom line. If you are not VAT registered, or you supply exempt products or services, then do take a look at their terms of service for further advice.
With the latest upgrade to Sage50c version 27.1.562.0 there is an additional setting required in Settings/Company Preferences/GoCardless and you need to set the tax code to use for Fees before GoCardless integrates correctly.
If anything I've written here resonates with you, call me on 01604 420057 and let's see how we can help you.