Payout Reconciliation for Ecommerce Teams

Ecommerce businesses deal with payouts from Shopify Payments, PSPs, and potentially multiple marketplaces — each with different timing, formats, and fee structures. Here is how to build a reconciliation process that works.

What makes ecommerce reconciliation complex

An ecommerce business might receive payouts from Stripe (for webshop orders), Shopify Payments (if separate), Amazon Seller Central (for marketplace sales), and Bol.com (for Dutch market sales) — each on a different schedule, with different fees and settlement formats.

Shopify Payments reconciliation

Shopify Payments aggregates payouts by payout period, which doesn’t correspond directly to order dates. Matching a Shopify payout to the underlying orders requires either using the Shopify API or working with the Payouts CSV export alongside the Orders export.

PSP settlement reconciliation

PSP settlement reports (from Stripe, Mollie, Adyen, etc.) typically contain individual transaction lines with gross amounts, fee deductions, and net payout. Matching these to orders in your ecommerce platform is the core reconciliation task.

Handling refunds and returns

Refunds add complexity because they typically appear in a settlement period after the original transaction. Connecting the refund to the original order and ensuring the correct net amount is reflected in your accounts requires careful tracking.

A workable reconciliation workflow

1. Import all settlement reports from each payment source. 2. Import order data from your ecommerce platform. 3. Match settlements to orders automatically. 4. Review exceptions and unmatched items. 5. Reconcile net payouts to bank deposits. 6. Export reconciled data to your accounting system.