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There should be a facility to automatically deduct processing fees, that are incurred for payments made online using credit/debit cards, e.g. Stripe, that incur an additional processing fee of 1.4% + 20 pence, per transaction.
We are also having the same issue, this is more of a problem now that we are MTD compatible as we are no longer able to edit invoices after a point in time and therefore have to create credit notes which is time consuming.
We had the same problem in our business - we have developed a plug-in that automatically imports and reconciles online Stripe payments. We are hoping to be able to offer this service to fellow KashFlow users if there is enough interest. Please let me know if you are interested (email : mark.pratt@ondemandsolutions.co.uk)
This would be very helpful