How to reconcile customer and supplier invoices and payments

What is it for?

Reconciling means linking what is owed with what was paid: a supplier invoice with the payment that settles it, or a receipt from a customer with the refund made to them. Once reconciled, the two sides no longer appear as an open balance in the customer's or supplier's current account.

This article covers the two cases fiscaldoo handles on screen: invoices, which are reconciled on the invoice itself, and other items of a customer or supplier (payments and manual journal entries), which are reconciled in the list of unreconciled items. Reconciliation with the bank statement is a different task: see How to reconcile bank movements.

When to use it?

• You registered a payment to a supplier or a receipt from a customer outside the invoice and the invoice is still unpaid.
• A customer overpaid or paid by mistake and the money was refunded: the receipt and the refund must cancel each other out.
• A customer's or supplier's current account shows small balances (cents) left over from rounding or discounts.
• Do not use the items list to reconcile an invoice: it does not show invoice lines (see step 1 and the notes).

Where to find it?

• Invoices: Accounting › Record › Purchases › Supplier invoices (or Sales and collections › Customer invoices), on the invoice form, the Outstanding debits (suppliers) or Outstanding credits (customers) notice.
• Items that are not invoices: Accounting › Reconcile › Banks and cash › Third-party reconciliation.
• Automatic reconciliation: Accounting › Reconcile › Banks and cash › What is there to do with the banks?, in the Supporting lists section, the Automatic third-party reconciliation line.

Before you start

• The profile is Accountant (or Fiscal officer). The Auditor can only consult: when trying to create a manual reconciliation, the screen answers “O seu perfil (Auditor) é só de leitura: consulta tudo e nunca cria, altera ou elimina nada.” (your profile (Auditor) is read-only: it consults everything and never creates, changes or deletes anything).
• The invoice is Posted and the payment is registered: a draft cannot be reconciled.
• Both sides belong to the same customer or supplier, the same account and the same company.
• If you are going to adjust a difference, first choose with your certified accountant the income or expense account where it goes.

How to use it

Reconcile an invoice with its payment

1. Open the supplier invoice (in the example, FTF/2026/00046, 300,00 € from Papelaria Central, Lda). The notice You have outstanding debits for this supplier listed below (Tem débitos pendentes listados abaixo para este fornecedor) says there are payments registered and not yet linked to an invoice. In the Outstanding debits section, choose the right payment (PBNK1/2026/00043, 300,00 €) and click Add.
2. The invoice becomes Paid, the Payments button shows 1 and the Amount Due is 0,00 €. The reconciliation creates no new journal entry: it only links the payment and invoice lines in account 2211.
3. If the payment differs from the total (in the example, 149,50 € for an invoice of 150,00 €), the invoice keeps an Amount Due equal to the difference (0,50 €). The rest has to be settled with another payment. The third-party reconciliation screen has no step to close the remainder of an invoice: the list only shows payments and manual journal entries, not invoice lines, so the 0,50 € difference stays on the invoice (Amount Due) until it is paid.

Reconcile items of a customer or supplier that cancel each other out

1. Open Third-party reconciliation. The Unreconciled third-party items list shows, by Account and then by Partner, the registered items with an open balance. Open the group for the account (2111 Clientes gerais) and for the customer (António Carlos Sousa (ENI)): there are two items, a collection of −123,00 € and its refund of 123,00 €.
2. Tick both lines, click Actions and choose Reconcile third-party items.
3. The wizard shows the Account, the Partner, the Open debit, the Open credit and the Difference. With 123,00 € on each side, the difference is 0,00 €: click Reconcile. Both items leave the list and the customer's group disappears.
4. If the two sides do not balance (in the example, 200,00 € received and 199,50 € refunded), the wizard shows the Difference (−0,50 €) and says: “The items do not balance: without an adjustment a partial reconciliation remains open.” If you do nothing else, clicking Reconcile links the lines but leaves 0,50 € open on the customer's account.
5. To close the difference, switch on Adjust the difference?, choose the Adjustment account and the Adjustment journal (it opens with Miscellaneous Operations), confirm the Description (“Reconciliation adjustment”) and the Adjustment date, and click Reconcile. fiscaldoo creates an adjustment entry in the chosen journal: in the example, D 2111 Clientes gerais 0,50 € and C to the adjustment account 0,50 €, and reconciles everything. Pending validation by a certified accountant: the income or expense account to which customer and supplier reconciliation differences are booked, and their tax treatment.

Reconcile several items automatically

1. Open What is there to do with the banks? and, under Supporting lists, click Automatic third-party reconciliation.
2. Under Criteria, choose the Accounts, the Third parties and the dates From and Up to you want to review; if you leave everything empty, fiscaldoo takes all customer and supplier accounts. In Tolerance, type the largest difference you accept to adjust (0,00 € by default, equal amounts only) and choose the Adjustment account; the Adjustment journal, the Description and the Adjustment date open already filled in. In the example: Third parties Cliente Teste Beta, SA, Tolerance 0,50 €. Without an Adjustment account, only equal amounts are reconciled.
3. Click Preview. The window gives the Match Count (1) and how many need an adjustment (With adjustment 1), and lists each pair: the account, the customer, the lines and the Difference (−0,40 €). Nothing has been reconciled yet; Back lets you correct the criteria.
4. Click Reconcile. The window now says Reconciliation done. and shows the list of what was reconciled. The adjustment entry was D 2111 Clientes gerais 0,40 € and C 7888 Outros não especificados 0,40 €. It is a gain for the company (the account is an income account): the customer balance was in the company's favour, as it received 200,00 € and refunded 199,50 € (in the first adjustment, 0,50 €, the entry uses account 7882 “Excesso da estimativa para impostos”, which does not describe this case: use an adjustment account of your own). Click Close. Pending validation by a certified accountant: the right adjustment account for reconciliation differences.

Expected result

• The invoice becomes Paid (or keeps an Amount Due equal to the difference) and the customer's or supplier's current account no longer shows the reconciled items.
• Reconciling without a difference creates no journal entries; with an adjustment, it creates an entry in the chosen journal (in the example, OD/2026/00104 and OD/2026/00105 in Miscellaneous Operations), which you can see in the ledger and in the partner statement.

Important notes

• The items list does not show invoices. It only shows payments and manual journal entries; invoice lines neither appear nor enter automatic reconciliation. To reconcile an invoice, use the Outstanding debits or Outstanding credits notice on the invoice itself.
• Each reconciliation covers a single third party, a single account and a single company. The wizard refuses anything else (see the common problems).
• The adjustment goes to profit and loss. Before adjusting, confirm with your certified accountant that a difference of that size can be booked as a gain or an expense. Pending validation by a certified accountant: limits and documentation of the difference.
• Reconciling communicates nothing to the AT.

Common problems

“Select at least two journal items to reconcile”

• Symptom: when you open Reconcile third-party items with only one line ticked, the wizard shows: “Select at least two journal items to reconcile. Open the list of unreconciled items, tick the debit and the credit items of the same third party and try again.”
• What to do: close the wizard, also tick the item on the other side and try again.

“The selected items belong to different third parties”

• Symptom: “The selected items belong to different third parties (or some have none). Third-party reconciliation needs one single partner.”
• What to do: tick only the items of one customer or supplier at a time.

“Some required fields are empty” when adjusting

• Symptom: with Adjust the difference? switched on and no Adjustment account, Reconcile shows “Some required fields are empty. Fill in the fields marked in red to be able to save.”
• What to do: choose the Adjustment account.

“There is nothing to reconcile with these criteria”

• Symptom: in automatic reconciliation, the preview gives Match Count 0 and Reconcile answers “There is nothing to reconcile with these criteria. Change the tolerance, dates or accounts and preview again.”
• Cause: the amounts are not equal and the tolerance is 0,00 €, or the Adjustment account is missing.
• What to do: Back, increase the Tolerance and choose the Adjustment account, or reconcile by hand.