Do you use a holding account for your Stripe payments?
It should be treated as a merchant account, in essence creating 2 transactions. You would have:
In your Stripe holding account:
- a money in transaction tagged to the invoice itself (e.g. £50.00)
- a money out transaction for the fee tagged to the Stripe invoice (e.g. £1.00)
- a money out transaction for the transfer tagged as a transfer to your current account (e.g. £49.00)
That way, each invoice has it’s own payment attributed to it, plus your bulk payments are tagged to coming into your current account in one go.
There’s a guide to merchant accounts here.
I hope that helps?