Status is treated as payment proof
A store can report an order paid without independently confirming that the provider captured the money.
WooCommerce · Reconciliation across payment methods
WooCommerce Payment Reconciliation as a Regular Routine
Reconciliation is a recurring control, not a one-off repair: every paid order should end with matching money from the method the buyer chose, and every payment should belong to an order. This guide sets up that routine across all your payment methods. For the Stripe mechanics behind one payment, see Stripe WooCommerce reconciliation.
Why a daily total is not enough
Matching totals can conceal order-level problems; different totals can also be legitimate.
Different operations are combined
A payout may include fees, refunds and payments from several days. It is not the original order amount.
Matching or coverage is incomplete
An unresolved reference, missing integration or stale import should lead to investigation, not a zero balance.
What each payment method gives you to compare
Reconcile each method against its own independent record. Where there is none, the result stays unknown — not “fine”.
| Payment method | Independent record | What to compare per order | Business Watchdog |
|---|---|---|---|
| Stripe (cards, wallets and other methods through Stripe) | Payment and charge in the Stripe account | Captured amount, currency, refunds | Automatic, restricted read key |
| PayPal (PayPal Payments) | Capture in the PayPal account | Capture status and amount, refunds | Automatic, reading methods only |
| Bank transfer | Your bank statement | Amount received and order number in the reference | Not covered — manual |
| Cash on delivery | Carrier’s cash report | Amount collected per shipment | Not covered — manual |
| Other gateways (Klarna, Mollie and others) | The provider’s own report | Report entries against orders | Not covered yet — shown as unknown |
A weekly routine that takes minutes, not hours
1. Close the period
Pick last week, one currency and live mode. Make sure every source has synchronized; note late imports instead of guessing.
2. Paid orders without money
Orders marked paid with no matching capture: check notification delivery and the payment reference before anything else.
3. Money without an order
Captures that no order claims: search the reference, other shops, staging copies and payment links.
4. Refunds on both sides
Every refund in WooCommerce needs a provider refund of the same amount — and every provider refund needs an order.
A repeatable order-level reconciliation workflow
- Choose one store, provider account, currency, mode and covered period. Confirm that all required sources have synchronized.
- Match the WooCommerce transaction reference to the provider’s payment and capture. Do not match solely by equal amount or nearby timestamps.
- Compare the order amount with captured funds. Then compare each reported refund with independent refund evidence.
- Review differences by type: missing capture, amount disagreement, unmatched reference or refund mismatch. Keep fees and payouts in a separate accounting task.
Official references for the checks above:
Resolve the type of difference you actually found
Resolve the confirmed cause
A missing webhook calls for a delivery repair; an unresolved reference calls for matching; a real amount difference calls for a review of the original order and provider operations. Keep a record of the evidence and choose the correction in the responsible system.
Verify the result
Run the comparison again after synchronization. Confirm that the particular discrepancy has cleared, rather than relying on the daily totals becoming equal. Do not offset an incorrect capture with an unrelated refund.
How Business Watchdog supports reconciliation
Business Watchdog reads WooCommerce orders and compares supported captures and refunds with independent Stripe or PayPal data. It highlights covered mismatches and explains incomplete or unmatched evidence without silently treating it as a healthy zero.
- Order and payment data are compared only within the connected, supported coverage.
- Missing or stale data is shown as incomplete, not as a healthy result.
- Alerts can be delivered by e-mail or Telegram when the corresponding supported rule applies.
Where the coverage stops
This is order/payment reconciliation, not bank payout reconciliation or a bookkeeping ledger. Fees are information rather than an order underpayment. Unsupported gateways and unverified matches do not become independently confirmed payments.
How to connect monitoring safely
- Create a WooCommerce read key and connect the store. Review the synchronization period and freshness.
- Connect the supported provider separately using the access instructions. Verify store attribution when an account serves several shops.
- Review the first reconciliation results and configure e-mail or Telegram notifications for the supported incident rules.
PayPal cannot provide strictly read-only credentials; Business Watchdog restricts its own requests and explains this before connection. Read the security and access details
Questions worth separating
Does a refunded order prove the customer received a refund?
No. The store’s refund record must be compared with independent provider evidence; manual refunds can require additional review.
Can I compare the bank deposit with total order sales?
Not as an order-level capture check. Deposits and fees have different timing and scope.
Related troubleshooting guides
Keep the next discrepancy visible
Connect your store and the supported payment provider. Review the coverage and first synchronization before relying on the results. Features and limits depend on your plan.