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Mollie or Stripe payments come in but VAT split is wrong

PSP integrations import the gross minus fees as one line by default. VAT lives in the original invoice, not in the payout batch.

Try this first

  1. 1Understand the flow first: invoice (with VAT line) and payment (PSP payout) are two separate events. The integration must match the PSP payout against the outstanding invoice, not compute VAT itself.
  2. 2In Moneybird/Yuki/Exact: set the PSP as a 'transit account' (often 1700-series). Incoming payment books on that transit account, transaction fees as costs, the difference matches the invoice.
  3. 3Hunt the mismatch: is there an invoice that deviates from PSP amounts? Often a manual edit to the invoice did not propagate to the integration.
  4. 4Multi-currency: a Mollie payout in EUR for a USD invoice creates an FX difference. That belongs in a separate 9xx account, not as discount or surcharge in the entry.
  5. 5For Stripe Billing subscriptions: proration (upgrade/downgrade mid-cycle) creates credit invoices. Verify those sync too, not only regular invoices.

When to bring us in

When period totals differ between VAT return and ledger: do not reconstruct yourself. An accountant with both ledger and PSP-export visibility fixes this more cleanly than a blind reimport.

See also

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