Reconciliation
Payment reconciliation
Connect store orders, provider payment records, payouts and bank deposits, then investigate timing differences, refunds, fees and unmatched amounts.
Payment reconciliation connects store orders, provider payment records, provider payouts and bank deposits. Match each payment event to an order, explain how the provider balance becomes a payout, then confirm what reached the bank. A paid order and a bank deposit are different events.
Reconcile at two levels
First, compare store orders with provider payment records. Keep the order ID, provider payment ID, capture and refund references, amounts, currencies, statuses and event dates. One order can have several payment attempts or financial events, so a single paid flag cannot explain the full payment history.
Next, reconcile the provider’s balance activity or payout batch with the bank statement. A payout can combine payments with refunds, fees, disputes, reserves and other adjustments. Use the payout ID or bank reference where available; do not expect a bank line for every order.
Check which report applies to the account’s payout arrangement. For example, Stripe’s itemised payout reconciliation report covers eligible automatic payouts, while instant payouts require a different approach.
| Record | Question it answers | Useful fields |
|---|---|---|
| Store order | What does the store record as paid? | Order ID, payment reference, amount, currency |
| Provider payment | What happened to the payment? | Payment ID, event type, amount, status |
| Provider balance or payout | Which entries affected the balance or transfer? | Balance entry, payout ID, net amount, currency |
| Bank statement | What arrived? | Deposit amount, date, currency, reference |
The Payout reconciliation and Ending balance reconciliation sections offer Summary downloads of dashboard totals and itemised downloads of every transaction included in those totals. CSV exports are available to all accounts, and custom metadata can be included to help match Stripe transactions with records in an accounting system.
Choose and export provider reports
Stripe’s Payout reconciliation report is available for accounts with automatic payouts, and for platforms with manual payouts when their Connected Accounts use automatic payouts. Stripe directs users with other manual payout arrangements, or those tracking their balance like a bank account, to its Balance report.
For Stripe automatic payouts, select a date range that includes the payout’s estimated arrival date; widen the range if that date is uncertain. The report groups transactions by payout and category, and its itemised CSV lists the payments, refunds, disputes, fees and other balance transactions included.
Separate report sections answer different questions: Stripe’s Balance summary shows starting and ending balances and period activity, while Payout reconciliation breaks down automatic payouts. Ending balance reconciliation shows transactions not yet settled by the report end date. A Failed payouts section appears only when failed automatic payouts exist in the selected period.
Pros and Cons of Automated vs Manual Payout Reconciliation
- Automated Payouts (e.g., Stripe, Shopify)Pros: Faster reconciliation, reduced manual effort, real-time reporting. Cons: Limited flexibility, may miss exceptions without review.
- Manual PayoutsPros: Greater control over timing and batch grouping. Cons: Higher risk of errors, requires more time and tracking.
Explain the balance and the deposit
For each provider account and payout currency, compare the opening balance with the closing balance after all signed balance entries and payouts in the period. Categorise payments, refunds, fees and adjustments without subtracting a fee twice if the provider has already included it in a net entry. Then trace each payout to the bank and investigate any transfer that has not arrived.
Keep the customer’s transaction currency separate from the payout currency. Where conversion occurs, retain both amounts and the provider’s conversion details. Use consistent reporting cut-offs and time zones; an order, capture and deposit may fall on different reporting days.
In Shopify Payments’ activity report, starting balance is the balance at the selected period’s start, and balance change from activity is the period’s net movement. Expanding that movement shows gross activity before fees and payouts, fees deducted, payouts to the bank and the resulting net amount.
The Shopify activity report describes movement in the provider balance, not sales timing. Its figures can differ from order-based sales activity because the two records can use different timing or totals, so keep the report’s purpose clear when reviewing a period.
Key Reconciliation Metrics for Australian Merchants
- Payout Currency
- AUD
- GST Inclusion
- Separate from transaction amounts
- Conversion Handling
- Retain both original and converted amounts
Use reports for period checks and hand-offs
Shopify Payments’ activity report presents balance activity for a selected date range and payout currency. It can support period-level review, month-end reconciliation and record keeping; use the Payouts page instead when checking a particular bank deposit.
The Shopify report requires Shopify Payments and permission to view payouts, held by the store owner or an authorised staff member. Each payout currency has a separate report when a business receives payouts in multiple currencies. The report excludes Shopify billing fees, third-party processors and third-party payment methods.
Check a report’s stated scope before treating it as a complete view of deposits or payment activity, especially where multiple providers or payment methods are involved.
Monthly Reconciliation Checklist for Shopify Payments
- Verify access to Shopify Payments reportsEnsure store owner or authorised staff have permission to view payouts.
- Select correct payout currencyRun separate reports for each currency if multiple are used.
- Exclude non-Shopify feesConfirm third-party processors and billing fees are not included.
- Compare balance movementCheck starting balance, activity change, and resulting net amount.
- Validate bank depositMatch payout ID to bank reference and deposit date.
Review exceptions
A paid order missing from a payout may still be pending, held, assigned to another payout or processed through another method or provider. A lower payout may reflect refunds, fees, disputes, reserves or adjustments. Check the underlying provider event before changing an order or accounting record.
Record each open difference, the references checked, its likely cause, who will investigate it and when it should be reviewed again. Give unexplained captures and failed payouts their own follow-up. Review new payment exceptions regularly, reconcile deposits as payouts occur, and revisit unresolved balances at period close.
This process traces payment funds. It does not, by itself, determine revenue, GST or the accounting treatment of a transaction.
Keep the provider, payout currency and report period with the review record so a later check uses the same account and reporting context.
In this guide
- Matching payment settlements with store ordersUse payment references, event amounts and payout batches to match store orders to settlements without confusing gross sales with bank deposits.
- Investigating orders marked paid without a matching settlementTrace a paid order through its payment method, capture status, provider balance, payout and bank deposit before classifying the difference.
- Handling partial captures and partial refundsKeep authorisations, successful captures and later refunds distinct so order changes and returns reconcile to the right payment events.
- Tracking payment fees by provider and methodBuild a fee view from provider transaction reports, separate account-level costs, and compare payment methods using consistent counts, value and currency.
