In QuickBooks Online, you match a SEPA payment in the For review tab of Bank transactions, choosing the invoice payment it settles from the matches QuickBooks suggests by amount and date. A deposit that bundles several direct debits needs those payments grouped first, in Undeposited Funds or a clearing account, with any fees the provider took recorded as an expense. Payments taken through Adfin are marked paid in QuickBooks automatically and paid out gross.
In this article
The short version
- QuickBooks suggests matches by amount and a similar date range.
- Group bundled direct debits in Undeposited Funds or a clearing account.
- Record provider fees as an expense so the deposit total agrees.
- Reopen the invoice if a collection is returned or refunded.
- Payments through Adfin are marked paid in QuickBooks and paid out gross.
How matching works in QuickBooks Online
Once your bank account is connected, QuickBooks Online downloads each transaction after it has cleared and lists it in the For review tab under Bank transactions. Where it finds a record that could fit, such as an invoice payment you've already received, it shows suggested matches with the same amount from a similar date range. You check the details, pick the right one and select Match. If the suggestion is wrong, Find other matches lets you search for the correct record.
A SEPA credit transfer from a customer usually arrives as its own line, for the amount the customer chose to send, with whatever reference they typed. If they paid the full invoice and quoted its number, the match takes a few seconds. The slower cases tend to be the ones QuickBooks can't suggest, because the amounts or dates differ from anything it holds: a part payment, a transfer covering two invoices, or a payment with no reference at all.
For those, record the payment against the invoices the customer meant, using any remittance they've sent, and leave any balance open. If you can't tell who paid, hold the money in a suspense account while you trace it, so you're not guessing and chasing the wrong client later.
When one deposit covers several direct debits
A SEPA direct debit works the other way round. You start the collection, so you know the amount and the date before the money moves. How it reaches your bank depends on the provider. Some pay out each day's collections as one sum, and some take their fees off before it arrives, which leaves a bank line that matches no single invoice.
QuickBooks' Undeposited Funds account exists for this. You receive each customer's payment against its invoice into Undeposited Funds, then make a bank deposit that groups those payments to equal the line in your bank feed. If the provider deducted fees, add them to the deposit as a separate line against an expense account, so the total agrees with what actually arrived.
Some accountants prefer a dedicated clearing account for each provider instead. Payments go in at their full value, fees come out, and the payout leaves it as a transfer to your bank account, so the clearing account should drop back to zero after every payout. A balance left in it tells you something hasn't been matched.
Say three monthly direct debits of €400, €250 and €150 are collected on the same day, €800 in total, and the provider's fees for that run come to €6 and it deducts them, so €794 lands in your bank. You'd record €800 of invoice payments, €6 of fees and a €794 deposit, and all three invoices show as paid in full.
Returned and refunded collections
A direct debit you've matched can still come back. A collection can come back unpaid, for example when the account is closed or short of funds. Your customer also has eight weeks from the debit date to get an authorised collection refunded by their bank, and 13 months if they say they never authorised it.
When that happens, record the money leaving your bank against the original invoice so it shows as unpaid in QuickBooks again, then add it back into your normal chasing. If you've already closed the month, agree with your accountant how a late refund should be posted, since the eight-week window can run past a month end.
What to ask a payment provider before you choose
How much matching you'll do each month depends a lot on how you collect. Before you sign up with a provider, it's worth asking:
- Does a payment taken through it get posted to QuickBooks against the right invoice, or do you match it from the bank feed yourself?
- Does it pay out gross, with fees invoiced separately, or net, with fees taken off each payout?
- Does each payout cover one payment or a batch, and does it give you a report listing what's in it?
- How does a returned or refunded collection show up, and does the invoice reopen in QuickBooks?
Adfin is a certified QuickBooks app with two-way sync. Payments your customers make through it, whether by SEPA direct debit, card, Apple Pay, Google Pay or bank transfer, are marked paid in QuickBooks automatically, and payouts arrive gross to an account in your business's own name, with Adfin's fees invoiced separately. On SEPA direct debit and bank transfer, each payment costs 20c + 1%, with the 1% part capped at €2, so the €400 collection above would cost €2.20. Card payments aren't capped, and there's no monthly fee, setup fee or contract.
Payments a customer sends straight to your bank, outside Adfin, still need matching in QuickBooks in the usual way. Adfin's collection agents can chase whatever is still open within rules you approve, and because payments are marked paid as they arrive, a customer who has paid through Adfin isn't reminded about that invoice.
Common questions
Why doesn't QuickBooks suggest a match for my SEPA payment? QuickBooks suggests records with the same amount from a similar date range, so a part payment, a combined payment or a deposit with fees taken off won't match on its own. Record the payments first, then match the bank line to them.
What is Undeposited Funds used for in QuickBooks? It holds invoice payments you want to combine into one bank deposit. You group them on the bank deposit screen so the total equals the line in your bank feed.
Should I record direct debit deposits gross or net in QuickBooks? Record each invoice payment in full and the provider's fees as an expense. The payments less the fees should equal the deposit.
What happens in QuickBooks if a customer reverses a direct debit? Record the money leaving your bank against the original invoice so it's unpaid again, then chase it like any other overdue invoice.
Does Adfin mark SEPA payments as paid in QuickBooks? Yes, Adfin is a certified QuickBooks app with two-way sync, and payments taken through it are marked paid in QuickBooks automatically. Transfers sent straight to your bank still need matching.
Does Adfin take its fees out of payouts? No, Adfin pays out gross to an account in your business's own name and invoices its fees separately, so the payout matches the invoices it covers.
Sources
- Intuit QuickBooks - Match online bank transactions in QuickBooks Online, Ireland (accurate as of November 2026) https://quickbooks.intuit.com/learn-support/en-ie/help-article/bank-feeds/match-online-bank-transactions-quickbooks-online/L6qyw0PvP_IE_en_IE
- Intuit QuickBooks - What's the Undeposited Funds account, Ireland (accurate as of November 2026) https://quickbooks.intuit.com/learn-support/en-ie/help-article/bank-deposits/whats-undeposited-funds-account/L6Jan3iRK_IE_en_IE
- Intuit QuickBooks - What are bank deposits in QuickBooks, Ireland (accurate as of November 2026) https://quickbooks.intuit.com/learn-support/en-ie/help-article/bank-deposits/bank-deposits-quickbooks/L4rH8Kg74_IE_en_IE
- European Payments Council - 2025 SEPA Direct Debit Core Rulebook, version 1.0 (accurate as of November 2026) https://europeanpaymentscouncil.eu/sites/default/files/kb/file/2024-11/EPC016-06%202025%20SDD%20Core%20Rulebook%20version%201.0.pdf
- Adfin - Pricing, Ireland (accurate as of November 2026) https://www.adfin.com/ie/pricing
