Money rarely arrives in the shape the invoice expected. One customer pays three invoices with a single round figure. Another pays half now and half in three weeks. A third overpays, because they’d forgotten about a credit note they were holding.
None of that is unusual, and all of it is where a simple “paid” tick box starts to lie to you. So there isn’t one. What an invoice has been paid is worked out from the payments actually applied to it, which means a part payment is just a normal state of affairs, and money you can’t account for yet stays somewhere you’ll see it.
What you can do
- Register a payment against a sales invoice or a purchase document, in full or in part.
- Spread one payment across several documents, and see how much of it went where.
- Keep money you haven’t applied yet as credit on the account, rather than forcing it onto a document where it doesn’t belong.
- Apply that credit later, against whichever open document you choose.
- Take payment through a link on the invoice: card or bank transfer, plus PayPal, iDEAL and UPI where your customers use them.
- Match payments automatically when you import your bank statement.
- Attach proof of payment when someone sends you a screenshot of the transfer.
- See how long you’re actually waiting to be paid, measured rather than estimated.
- Find money you’ve received but can’t yet identify, sorted by how long it’s been sitting there.
- Print a check for a supplier, on the pre-printed check stock you already buy.
- Pay suppliers by ACH: pick the payments, and get the file your bank’s portal takes.
How it works in practice
Register what arrived (the document → Payments → Register). Enter the amount, the date and how it came in. It gets applied to that document up to whatever’s still owing. If your customer sent more than the document needs, the extra isn’t forced onto it. It sits on their account as credit, and the screen tells you it’s there.
Apply that credit when you’re ready. An account holding credit shows an Apply button the next time you register a payment against one of its documents. Take all of it or part of it, and it draws from the oldest credit first, which is what an accountant would do by hand.
Let the bank do the matching (Finance → Bank). Import a statement and each line is offered against the open documents it might settle. Confirm a match and three things happen at once: the payment is registered, the document’s balance updates, and the journal gets written.
Money you can’t place goes somewhere sensible. When a payment turns up with a reference nobody recognizes, we don’t guess. It goes to a holding account and appears on its own list (Reports → Finance → Unidentified Receipts), grouped by age: under 30 days, 30 to 60, and older. Each line has an Identify button that takes you to the statement line to sort it out. The idea is that unidentified money becomes a short list someone works through, instead of a difference you discover at year end.
Get paid without waiting for a transfer. Connect a payment provider and your invoices can carry a link. Your customer pays it, and the payment shows up against the invoice on its own. Nobody re-keys anything, and nobody has to notice it happened.
Pay a supplier by check (Procurement → Payments). Register the payment against the bill with the method Check, then choose Print check on its row. You get a PDF for standard “check on top” voucher stock: the check itself, with the amount in figures and in words, and two stubs listing the bills it pays. Numbers run on from your bank account’s sequence, starting at 1001 for a new box. A reprint keeps the same number.
Pay suppliers by ACH (Procurement → Payments → Create ACH file). Record each payment with the method ACH, and the list shows every one that isn’t in a file yet, along with anything stopping it: a missing routing number, one that fails its check digit, a bill in another currency. Tick the payments, choose the day the money should arrive, and upload the file to your bank. Your bank moves the money; we write the instructions. Set it up once: your routing number and the ACH company ID your bank gave you on the account you pay from (Settings → Finance → Banks), and each supplier’s routing number and account type on their bank details.
Watch the ageing. Every payment records how many days it took from the document date, so days sales outstanding is something you measure rather than model. You’ll find it on the invoice reports, alongside what’s still open and what’s expected in the next thirty days.
Good to know
- An overpayment never quietly disappears. It becomes credit on the account and keeps asking to be dealt with. Test this in your first week: it’s the difference between a system that records what happened and one that records what somebody assumed.
- Two accounts do the quiet work - a holding account for unidentified receipts, and one for customer advances. If you don’t nominate accounts from your own chart, they’ll be created for you. Nominating them yourself takes ten minutes and keeps your chart looking like yours.
- Automatic matching is only as good as the reference your customer typed. Structured bank formats match far better than a statement where each line says whatever the bank printed, and the manual route is there for everything else.
- Payment links need a provider account of your own - PayPal, Mollie or a UPI address, set up once. There’s no shared merchant account and nothing is taken here. You get paid through your own provider, on their terms. Which providers suit you depends on where your customers bank: Mollie covers European methods like iDEAL, and UPI is India.
- Checks print onto pre-printed stock, not blank paper. Your bank’s details and the magnetic-ink line along the bottom come on the stock, because a bank’s sorting machines reject that line printed in ordinary toner. Checks print one at a time, and a voided check isn’t recorded here yet.
- Each ACH payment goes into one file, once. Putting a payment in a file marks it, so the next file leaves it out and nobody gets paid twice. If a file never reached your bank, you can rebuild it, and you’re warned first. And if one payment in a batch can’t be sent, no file is written at all: every reason is listed instead, because a file that quietly dropped a supplier looks exactly like one that paid everyone.
- ACH dates skip weekends, not bank holidays, and the file carries credits only. If your bank asks for a balanced file with an offsetting debit, check with them first.
- Deleting a payment releases what it was applied to, and those documents go back to owing what they owed. That’s correct, but it’s also why a payment entered against the wrong customer is worth fixing straight away rather than working around.