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Your online store shows AED 20,000 in card payments. The bank shows a deposit of AED 18,650. Before you chase a missing payment or adjust the sales figure, open the processor’s settlement report. It should show which payments went into the deposit and which fees, refunds or other adjustments came out of it.
That check is called payment gateway reconciliation. You match your store’s payment records to the gateway’s settlement report, then match the settlement to the deposit in your bank account. Keeping all three records together makes it much easier to explain a difference at month-end.
How the payment gateway reconciliation process works
For UAE online stores, payment gateway reconciliation has two checks. The first links individual customer payments to the gateway’s transaction records. The second links the resulting settlement to the actual bank deposit. A payout can match the bank perfectly while the store’s internal records still contain a missing refund or a duplicate payment.
Match orders to payment gateway transactions
Filter the order export to the payment method you are checking. Compare each captured amount and currency with the payment gateway report. Use the gateway transaction ID where you have it. The same customer may have placed two orders for the same amount, so matching on amount alone can create false matches.
Check status before investigating missing transactions. An authorisation may appear in the payment gateway before any funds are captured. Keep captured, refunded and cancelled payments in separate groups so you can follow the right records.
Match settlement batches to bank statements
Group the gateway transactions by payout ID, then check the net total against the deposit shown on the bank statement. Compare amounts in the same settlement currency and retain the bank reference. When a payout appears as sent in the portal but has yet to reach the bank account, leave the item open until you can verify the deposit.
Payment gateway reports and bank statements to collect
| Record | What to look for |
|---|---|
| Store order and payment export | Order number, payment reference, amount, currency, refunds and payment status |
| Gateway settlement report | Payout ID, included transactions, fees, refunds, disputes, adjustments and net payout |
| Bank statement | Date the deposit posted, bank reference, currency and amount received |
Start with one bank deposit and work backwards. Find the corresponding payout in the gateway report using the amount, currency and reference where available. Check the dates too. A gateway may show when it sent a payout, while the bank shows when it arrived.
If your Shopify store uses a separate payment provider, get the settlement report from that provider. Shopify’s Shopify Payments activity report covers transactions processed through Shopify Payments. For Stripe automatic payouts, the itemised payout reconciliation report shows the transactions that make up each batch. For manual payouts, Stripe directs users to its Balance report. Shopify payout reporting · Stripe payout reconciliation
Worked AED example of payment gateway reconciliation
Here’s how the opening example might look for one AED payout. The figures are illustrative and assume there are no other adjustments.
| Payout item | Amount |
|---|---|
| Card payments included in the batch | AED 20,000 |
| Refunds deducted | −AED 800 |
| Processing fees deducted | −AED 350 |
| Disputed payment deducted | −AED 200 |
| Expected bank deposit | AED 18,650 |
| Bank deposit received | AED 18,650 |
| Unexplained difference | AED 0 |
The payout explains the bank deposit. Your books still need the underlying activity recorded in the appropriate accounts. If the original sales are already posted, a common setup is to match the deposit against a payment gateway clearing account, which tracks money the processor is holding or sending to you. That way the deposit clears the balance instead of creating a second sales entry. Ask your accountant how refunds, disputed payments and any VAT amounts should be recorded for your setup.
Four reasons bank deposits differ from settlement records
- Payout date and bank date. If the gateway sent the money on 30 April and the bank posted it on 2 May, keep a record of the payout in transit and confirm it against the May statement.
- Refunds and disputes from earlier orders. A refund for a March order can reduce an April payout. Use the refund or dispute reference to trace it back to the original payment and check whether any amount was later returned.
- Different payment channels or currencies. Reconcile each provider and settlement currency on its own first. Keep cash on delivery and marketplace settlements separate from your card gateway batches.
- Reserves, adjustments or failed payouts. Check the provider’s status and balance reports for funds held, released or returned. Give unexplained differences an owner and a follow-up date so they stay visible.
How to resolve common payment reconciliation discrepancies
Duplicate transactions in the bank feed
If your accounting software imports both the payment gateway payout and the bank deposit, check whether the two entries represent the same transfer. Match them using the payout ID or bank reference. Review the general ledger entry before removing or reversing anything, especially if the original customer payments have already been recorded.
Currency conversion and processing fees
Keep the order currency, settlement currency and actual bank deposit in separate fields. For example, an order paid in US dollars may settle to a UAE bank account in AED. Use the provider’s settlement data to trace the conversion. If the bank deducted a separate charge, save the bank record that shows it and flag the difference for review.
Refunds, chargebacks and reserve releases
A refund can reduce a later settlement even though the original sale was reconciled last month. A chargeback may also have its own fee or a later reversal. Keep those movements on separate lines in your transaction records and link them to the original payment. If a provider releases a reserve, match that release to the earlier hold so the movement stays traceable.
Close the month with a short list of open items
Keep one row per payout in a reconciliation sheet. Record the provider, payout ID, settlement currency, expected deposit, actual deposit, bank date and any difference. Link each row to the gateway export and add a note for amounts still in transit or under review.
For example, if AED 2,400 in captured payments is still waiting to be paid out at month-end, record the amount as outstanding in your reconciliation and verify it when the next payout arrives. At the next close, revisit each outstanding item and mark it as cleared only after you can explain where the money went.
Set up a payment reconciliation worksheet
Use a payout tab for the bank match and a transaction tab for the detail. In the payout tab, enter the processor, payout ID, bank reference, expected net amount, deposit date and actual amount received. Calculate the difference by subtracting the expected payout from the deposit. If the bank has yet to post it, mark it as pending and leave the actual amount blank.
In the transaction tab, keep one line for each item in the processor’s export. Include the payout ID, order or payment reference, transaction type, currency and amount. Keep fees and refunds visible as separate rows or columns, depending on the export. The net total of those items should agree with the payout for that batch.
Use a consistent reference when the same order has several records. For example, an order might have two captures and one partial refund. The order number groups those entries, while the gateway transaction IDs help you avoid counting one of them twice.
Payment reconciliation best practices for month-end
Keep a record someone else can follow
Save the order export, payment gateway reports and bank statements for the period in a shared folder with restricted access. Give each exception a short explanation, an owner and a review date. This creates an audit trail and lets the next reviewer see why a difference was carried forward or cleared.
Review the clearing balance before closing the period
Check whether the balance in your payment gateway clearing account can be explained by open payouts, reserves or other documented movements. Once your finance team has reviewed the balance and agreed the entries, use the period lock in your accounting system if available. Route later adjustments through the normal review process so they remain visible.
When should you automate payment gateway reconciliation?
A spreadsheet can work for a store with one gateway and a manageable number of settlements. If you’re matching several payment providers or spending hours on the same exports each week, look for an integration that can import transaction IDs, fees, refunds and payout references into your accounting software.
Test one completed payout before turning on automatic posting. Compare the integration’s totals with the processor’s report and check that the bank feed matches the settlement without recording the sales again. Give someone responsibility for reviewing the exception list, especially when a provider withholds funds, changes its export or settles in a different currency.
Standardise the exports before using automated reconciliation
Different payment gateways can label the same field differently. Map each settlement file to a consistent set of columns for payout ID, payment reference, gross amount, fee, refund, currency and net amount. Test the mappings against completed payouts from each provider before using them on a live bank feed.
Use automated payment reconciliation to match records with reliable IDs and send exceptions to a reviewer. Manual reconciliation still helps with split deposits, missing references and unusual adjustments. Check the exception report regularly, especially after a provider changes its export format.
What if a deposit combines several payouts?
Check the bank reference and the processor’s settlement summary before splitting the deposit in your books. If the references are incomplete, list the candidate payouts in the same currency and check whether their combined net amounts agree with the deposit. Keep the supporting references together so someone else can retrace the match.
If online sales, processor fees and bank deposits are getting mixed together in your books, A&A’s accounting services in Dubai can help you set up a repeatable reconciliation and review the open items as part of your monthly reporting. Start with one store export, one gateway settlement report and the matching bank statement.
