Usually because the direct debit amount was set once, as a fixed subscription or plan, and your invoice has changed since. When a client adds seats or uses more telecoms minutes, the invoice in Xero or QuickBooks goes up but the direct debit keeps collecting the old figure. The lasting fix is to collect the amount on each invoice rather than a separate fixed amount.
In this article
The short version
- A direct debit usually collects the wrong amount because it was set as a fixed figure and the invoice has changed.
- A client moving from 22 to 25 seats at £48 a user leaves £144 unpaid if the old amount is collected.
- Collect any shortfall with notice, a payment link or on the next invoice, and refund overpayments promptly.
- A monthly check before the collection run works but relies on someone doing it every time.
- Collecting the amount on each invoice removes the second figure that goes out of date.
Where the mismatch comes from
A direct debit mandate gives you permission to collect from a client's account. The amount and date of each collection are set separately, and many setups let you create a recurring subscription for a fixed sum. That works well for a flat monthly fee, and less well when your invoices move with the client.
The usual causes are:
- A fixed monthly subscription set up at onboarding that nobody updated when the seat count changed.
- A mid-month change, such as new starters or extra licences, that went on the invoice after the collection amount had already been submitted.
- Usage charges, like telecoms minutes or extra storage, that vary every month while the direct debit doesn't.
- A credit note or discount applied to the invoice but not to the collection.
- An invoice edited after it was sent, so the collection follows the original figure.
In each case the invoice is right and the collection is wrong, or the other way round. Either way the two no longer match, so the invoice shows as part paid or overpaid and someone has to work out why.
A seat change in numbers
Say a client pays £48 a user a month including VAT, and starts the year on 22 users. Their direct debit is set up for £1,056. In March they take on three new staff, so the March invoice is for 25 users, or £1,200.
If the subscription still says £1,056, that's what gets collected. The invoice is left with £144 outstanding, which is exactly the three new seats. Nothing has failed, so you won't get an alert, and the gap tends to surface weeks later as an aged balance or a query from the client's bookkeeper.
It can run the other way. If two users leave and the invoice drops, the old amount over-collects, and your client is likely to notice before you do. Over-collecting tends to be the more awkward problem, because the client sees money leave their account that they didn't expect.
How to put a wrong collection right
Start with the invoice, since that's the figure you and the client agreed.
If you collected too little, you have three options. You can raise a second collection for the difference, giving the client advance notice of the date and amount first. You can add it to next month's invoice, clearly shown. Or you can send the client a payment link for the balance. For £144, any of these is fine, as long as the client knows what the extra amount is before it leaves their account.
If you collected too much, refund the difference or agree with the client to credit it against next month, and confirm it in writing. Every Direct Debit Instruction carries the Direct Debit Guarantee, which promises a full and immediate refund from the payer's bank if an error is made, so it's better to sort it out with the client before they go to their bank.
Then update the subscription amount so next month is right, and note who changed it and when.
How to stop it happening every month
If you stay with fixed amounts, the safest routine is a monthly check before the collection run: compare each client's draft invoice with their scheduled direct debit, update anything that differs, and give notice of the new amount. It works, but it relies on someone doing it before the cut-off every month, and per-seat billing means there's nearly always something to change.
The more lasting fix is to stop keeping two figures. When the direct debit collects whatever is on the invoice, a seat change on the invoice is a seat change in the collection, and there's nothing to reconcile by hand.
That's how Adfin's direct debit works. Mandates aren't tied to a fixed amount or date. Each collection uses the amount and due date of the invoice in Xero or QuickBooks, so the March invoice for 25 users collects £1,200. The client is told the date and amount at least three working days before each payment, and the invoice is marked paid in Xero or QuickBooks automatically once it's collected. Collection and any follow-up run through Adfin's collection agents, working within rules you approve.
Common questions
Can a direct debit collect a different amount each month? Yes. One mandate can cover collections of different amounts, as long as the client is told the amount and date in advance.
Does the client need to sign a new mandate when the amount changes? No. The mandate stays in place; only the notice for each collection changes.
How much notice do I have to give before changing a direct debit amount? The Bacs default is 10 working days unless you've agreed a different period with the client. Providers often agree a shorter period with the client at sign-up.
What should I do if I over-collected from a client? Tell the client, refund the difference or agree to credit it against the next invoice, and confirm it in writing. Under the Direct Debit Guarantee a client can ask their bank for a refund if an error is made.
Why does my invoice show as part paid after a direct debit? The collection was for less than the invoice, usually because the direct debit amount was set before seats or usage changed.
How do I collect the difference from a client? Raise a second collection with advance notice, add it to the next invoice, or send a payment link for the balance. With Adfin you can send that link by email, SMS or WhatsApp, and the client can pay by card or pay by bank.
Sources
- Bacs - Glossary (accurate as of October 2026) https://www.bacs.co.uk/resources/glossary/
- Pay.UK (Direct Debit) - The Direct Debit Guarantee (accurate as of October 2026) https://www.directdebit.co.uk/direct-debit-explained/direct-debit-guarantee/
- Adfin Help Centre - Getting started with direct debits (accurate as of October 2026) https://support.adfin.com/en/articles/10192945-getting-started-with-direct-debits
- Adfin - Accept payments (accurate as of October 2026) https://adfin.com/accept-payments
