Give each assignment its own invoice, with the job reference in the description and the invoice number as the payment reference, then allocate every payment in your practice system to the invoice it settles, not to the client's oldest balance. Split part payments and lump sums using the client's remittance, or ask them. Payments taken through a tool tied to a specific invoice, such as Adfin with Xero or QuickBooks, arrive already marked against that invoice.
In this article
The short version
- Raise a separate invoice for each assignment.
- Ask clients to quote the invoice number and nothing else.
- Allocate payments to the invoice named, not the oldest one.
- Split lump sums using the client's remittance, or ask them.
- Payments through Adfin are marked against the specific invoice in Xero or QuickBooks.
Why the allocation matters for WIP and time recovery
In a practice, a fee payment also closes off the work in progress on an assignment, and your recovery figures for the audit, the accounts, the tax return or the payroll depend on the payment landing against the right one. If a client pays €900 and it's allocated to whichever invoice is oldest, the job they meant to pay for still shows as unpaid, and the one you hadn't expected to be paid yet looks settled.
The knock-on effects build up quietly in your reports. Recovery on one assignment looks better than it was and another looks worse, a partner may write off time on a job you've been paid for, and you can end up reminding a client about the invoice they've just settled.
Practice management systems handle allocation in different ways, and some will allocate to the oldest invoice by default unless you choose otherwise. It's worth checking how yours behaves before you change anything else.
Set up invoices so each payment points to one job
The easiest payment for you to allocate is one that names a single invoice for a single job. A few habits make that the normal case:
- Raise a separate invoice for each assignment, even for the same client in the same month, with the assignment type and period in the description, such as "Year-end accounts, year ended 31 December 2025".
- Use the invoice number as the payment reference. Revenue requires a unique sequential number on every VAT invoice, so it already identifies the job without anything extra.
- Keep the reference short and free of extra words. A SEPA credit transfer carries up to 140 characters of remittance information, and a bare invoice number is easy to spot on the bank line.
- Print the invoice number next to your bank details with a line asking the client to quote it, and nothing else, when they pay.
- If a client pays several invoices at once, ask for a one-line email listing the invoice numbers.
If you collect monthly fees by SEPA direct debit, you start each collection against an invoice, so allocation is rarely the problem there. Your work tends to sit with one-off fees your clients pay by bank transfer.
Part payments, lump sums and statements
Say a company client of yours has three open invoices: €4,800 for the audit, €900 for the corporation tax return and €150 for October payroll. They send €3,000 with the reference "fees".
If the audit invoice is the oldest and you allocate that way, the whole amount goes against the audit. If the client meant to clear the tax return and payroll and put the rest towards the audit, the correct split is €900, €150 and €1,950, which leaves €2,850 open on the audit. Your recovery on the tax and payroll jobs then reads as complete, and the audit shows the true balance outstanding.
When there's no remittance, ask before you allocate. Until you hear back, hold the payment as unallocated on the client's account, which most systems allow, so it doesn't distort any single job.
A statement can head off some of this. Sending your client a list of open invoices, each with its own number and job description, gives them something to pay against and makes it more likely they'll tell you which items a payment covers.
Where a payment tool can help
A payment that starts from a specific invoice doesn't need you to allocate it by hand. With Adfin, each invoice gets its own payment link, sent by email, SMS or WhatsApp, and the client can pay by card, Apple Pay, Google Pay or bank transfer. Statements can carry several invoices for a client to pay together, and each payment is recorded against the invoice it settles. Adfin is a certified Xero app and a certified QuickBooks app with two-way sync, so payments taken through it are marked paid against those specific invoices automatically.
If your fees are raised in practice software that isn't Xero or QuickBooks, you can still send invoices into Adfin by forwarding the invoice email or uploading the PDF, and the invoice reference carries through, so in Adfin each payment sits against the fee note it settles. You'd still record the payment in your practice system yourself. Adfin's collection agents can then chase whatever is still open within rules you approve, so a client who has paid one job isn't reminded about it.
On SEPA direct debit and bank transfer, each payment costs 20c + 1%, with the 1% part capped at €2, so the €900 tax fee above would cost €2.20 by bank transfer. Card payments aren't capped, and there's no monthly fee.
Common questions
Should a practice allocate a payment to the oldest invoice? Only if the client agrees or tells you to. Otherwise allocate it to the invoice they name, so each job's recovery and work in progress stay accurate.
What reference should clients use when paying fees? The invoice number, and nothing else. It's unique to each invoice, so a payment quoting it points to one job.
How do I allocate a payment that covers several jobs? Split it across the invoices named in the client's remittance. If there's none, ask the client and hold the payment as unallocated until they reply.
Should each assignment have its own invoice? Separate invoices per assignment make each payment easier to allocate and keep recovery figures accurate job by job.
Can Adfin take payment for invoices raised outside Xero or QuickBooks? Yes, you can forward invoice emails or upload PDFs to Adfin and collect against them. The invoice is still raised in your own software, and the payment keeps its invoice reference.
Does Adfin mark payments against the right invoice in Xero and QuickBooks? Yes, payments taken through Adfin are marked paid against the specific invoice in Xero or QuickBooks automatically, through two-way sync.
Sources
- Revenue - What information is required on a VAT invoice? (accurate as of November 2026) https://www.revenue.ie/en/vat/vat-records-invoices-credit-notes/invoices/information-required-vat-invoice.aspx
- European Payments Council - Quick Response Code: guidelines to enable data capture for the initiation of a SEPA Credit Transfer, version 3.0 (accurate as of November 2026) https://europeanpaymentscouncil.eu/sites/default/files/kb/file/2022-09/EPC069-12%20v3.0%20Quick%20Response%20Code%20-%20Guidelines%20to%20Enable%20the%20Data%20Capture%20for%20the%20Initiation%20of%20an%20SCT_0.pdf
- Adfin - Pricing, Ireland (accurate as of November 2026) https://www.adfin.com/ie/pricing
