Part of the power of Bill Pay is that it automatically reconciles for you. When you make a payment through Apron, we post a record of that payment straight to your accounting system - marking the corresponding invoices as paid and keeping your books up to date without extra manual steps.
Sometimes though, you may notice that one or more invoices paid in Apron aren’t automatically marked as paid in your accounting system. This can happen for several reasons, but most often it’s because an invoice was accidentally made non-payable in Xero or QuickBooks between when you initiated the payment in Apron and when the payment was completed.
We’ll walk you through how to handle this - a few simple steps to make sure those invoices are correctly reflected as paid, so your books stay clean and everything reconciles.
Why this happens
When you pay invoices in Apron, we automatically post matching payment records to your accounting system. However, if one of those invoices becomes non-payable (for example, voided or deleted) we won’t be able to mark it as paid.
It’s important to note that the payment itself has still gone through - your supplier has been paid in full, and we reflected in Apron. The only issue is that your accounting ledger doesn’t yet reflect the payment made against that invoice.
What you’ll see
In your accounting system (Xero or QuickBooks), you might notice that:
The total payment amount doesn’t fully reconcile - part of the payment appears unmatched.
Payments for most invoices in a batch were recorded successfully.
One or more invoices paid in Apron show as unpaid or voided.
In action:
You paid £400 to four suppliers through Apron. If one of those bills was voided in your accounting system, only £300 (three invoices × £100) will be automatically marked as paid. The remaining £100 is still accounted for as paid in Apron, but it won’t be showing as paid in your ledger.
How to fix it
Follow these steps to make sure the full payment is correctly reflected, and your books are clean:
1. Review the payment record
In your accounting system, open the payment account you used, for example your HSBC account, and locate the payment line that matches the total amount of the Apron payrun (e.g. £400).
2. Identify which payments were successfully posted
Use the payrun reference from Apron to find and match the individual payments that were successfully posted to your accounting system. These will add up to less than the full amount of the batch (for example, £300 of a £400 payrun).
You can always confirm which invoices weren’t able to sync directly within Apron - they’ll be shown in the payrun details view.
3. Record the unmatched amount as a supplier overpayment
For any invoices that couldn’t be marked as paid, we recommend recording a supplier overpayment in your accounting system. This will allow the total payment amount to reconcile in your ledger and show that the supplier has already been paid.
When creating the overpayment:
Select the same supplier who received the payment.
Use the same payment account or method that was used for the transaction.
Enter the payment date that matches when the payment was made in Apron.
Add a reference (e.g. the payrun ID) and a short description such as “Invoice paid via Apron - awaiting replacement bill.”
Set the amount equal to the portion of the payrun not applied to an invoice.
4. Recreate the invoice and apply the overpayment
Finally, address the missing invoice in your accounting system:
If the original invoice can still be updated, simply edit it so it’s payable again.
Otherwise, create a new invoice for the same supplier, either via Apron or directly in your ledger.
Once it’s created, allocate the existing overpayment to the new invoice to mark it as paid.
The end result
The total payment is fully reconciled.
All invoices, including any recreated ones, are correctly marked as paid.
Your supplier ledger stays clean and accurate, with no duplicate payments or unallocated balances.