How to reconcile EFT payments to invoices (without losing a day)

To reconcile EFT payments, take every deposit on your bank statement and match it to an open invoice using, in order, the payment reference, the exact amount and the customer's name, then record the payment against that invoice and investigate anything left over. Do it daily or weekly, not at month-end, and make unique invoice references the default so most matches are automatic.

Manual EFT is cheap to accept but expensive to reconcile. The goal is to make 80–90% of matches mechanical and spend human time only on the exceptions.

Why EFT reconciliation is hard

• Customers type the reference themselves, and often get it wrong, shorten it, or use their own name.
• One deposit may pay several invoices, or one invoice may be paid in several deposits.
• Amounts don't match when customers deduct bank charges, round off or pay an old balance.
• The deposit description on your statement may show the payer's bank-account name, not the customer name you know.

The matching hierarchy

Use this order for each deposit:

Write these rules down so anyone on the team reconciles the same way.

Step-by-step routine

1. Get the bank data in

Use a bank feed or download a CSV statement. Avoid retyping deposits from a PDF. Only work with cleared deposits.

2. Pull the list of open invoices

Include customer name, invoice number, reference, amount outstanding and due date.

3. Auto-match the easy ones

Anything that matches reference and amount exactly gets recorded and closed. Good software does this for you.

4. Work the exceptions

• Part-payments: allocate to the referenced invoice, leave the balance open, and tell the customer what's outstanding.
• Overpayments: allocate to the invoice and hold the excess as a credit on the customer's account; refund or apply to the next invoice by agreement.
• One deposit, several invoices: allocate oldest first unless the customer specified otherwise (a remittance advice helps).
• Deductions for bank charges: decide a policy. Many businesses write off small differences below a threshold (for example R10) to a bank charges account.

5. Park the unidentified

Put unidentified deposits in a suspense (unallocated receipts) account, never against a random invoice. Then:

• Check for recently uploaded proofs of payment (see EFT proof of payment).
• Search open invoices for the amount.
• Ask your bank for more payer details if needed.
• Clear the suspense account every month.

6. Confirm and communicate

Send receipts for matched payments. Customers who get receipts are less likely to pay twice or to query later.

7. Review the aged receivables

After reconciling, the invoices still open are genuinely unpaid. Feed them into your credit control process.

Reconciling gateway and debit order settlements

Not every deposit is a single customer payment. Payment gateways and debit order providers pay out batches, net of fees:

• Match the settlement to the provider's payout report, not to individual invoices.
• Record gross customer payments against invoices (usually done automatically via webhooks), fees as an expense, and retention as a receivable from the provider.
• Check that the net deposit on your bank statement equals gross collections minus fees minus retention plus released retention.

We cover the bank side in bank reconciliation basics.

Make tomorrow's reconciliation easier

1. Unique references on every invoice and a clear instruction: "Use INV-10482 as your reference." See payment reference best practice.
2. Customer-level references for recurring customers, so all their payments land in one place.
3. Push people to self-confirming methods: payment links, instant EFT and debit orders reconcile automatically.
4. Reconcile frequently. Ten minutes daily beats a lost day at month-end.
5. Keep an audit trail of who matched what, especially for manual allocations.

Signs your process is broken

• Your suspense account keeps growing.
• Customers receive reminders for invoices they've paid.
• Month-end close waits on "finishing the recon".
• Only one person knows how it's done.

How CentraPoint helps

CentraPoint gives each invoice a unique reference, marks gateway and debit order payments paid automatically, and lets customers upload proof of payment against EFT orders for your team to approve. Its reconciliation module helps match bank deposits to invoices and flags what's still unallocated, and paid invoices can sync to Xero, QuickBooks, Zoho Books or Sage. See the reconciliation docs.

Frequently asked questions

How often should I reconcile EFT payments?

At least weekly, and daily if you receive many EFTs or release goods on payment. Frequent reconciliation keeps customer statements accurate and makes month-end quick.

What should I do with a deposit I can't identify?

Record it in a suspense or unallocated receipts account, look for a matching proof of payment or open invoice amount, and ask your bank for payer details if needed. Don't allocate it to a guess.

Should I refund an overpayment or keep it as credit?

Either, depending on your terms and the customer's wishes. Hold it as a credit on the customer's account until you agree, and refund only to the account it came from.

Is reconciliation the same as bank reconciliation?

They're related. Payment reconciliation matches receipts to invoices; bank reconciliation checks that your accounting records agree with your bank statement.