Reconciles

Shopify payout reconciliation for orders, refunds and fees

Reconciles automates Shopify payout reconciliation. You export payout transactions from Shopify Payments, upload them with your bank statement, and Reconciles matches every payout to its deposit, splits it into orders, refunds, chargebacks and fees, and exports the entries that keep revenue and costs in the right accounts.

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Why Shopify sales never equal your bank deposits

Shopify reports your sales by order. Shopify Payments pays you in payouts that bundle several days of orders, minus processing fees, minus refunds, minus chargebacks and adjustments. Your bank shows only the net payout. When finance compares the sales report, the payouts and the bank, three different totals come out for the same week.

  • Fees are deducted before the money arrives, so revenue looks smaller in the bank than in Shopify.
  • Refunds and chargebacks from earlier orders reduce later payouts.
  • Orders paid through PayPal or other gateways do not appear in Shopify Payments payouts at all.
  • Gift cards, discounts and shipping change what an order is worth.

If the payout is booked as one revenue line, fees and refunds disappear inside it and margins look better than they are.

How to reconcile Shopify payouts with Reconciles, step by step

  1. 01 Export payout transactions from Shopify

    In Shopify admin, open Finances, then Payouts, select the payouts for the period and export the transactions as CSV. Download your bank statement for the same period from your bank. If some orders are paid through PayPal, export the PayPal activity report as well.

  2. 02 Upload the payout export and the bank statement

    Drop the bank statement in the first slot and the Shopify export in the second. Reconciles reads the payout date and id, the transaction type, the order reference, the amount, the fee and the net amount of every line.

  3. 03 Review matches and exceptions

    Every payout is rebuilt from its transactions and matched to the bank deposit with the reason "payout batch net of fees". Orders can be matched to your ledger or invoices in a second run. A payout that does not add up, a deposit with no payout or a refund with no original order goes to the exceptions queue with the difference shown.

  4. 04 Export entries back to your ledger

    Approved journal entries book gross sales to revenue, processing fees to their cost account, refunds and chargebacks against revenue, and the clearing account back to zero. Import the CSV into QuickBooks, Xero or NetSuite after review.

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What Shopify payout reconciliation with Reconciles covers

  • Shopify Payments payouts vs bank deposits.
  • Orders vs revenue entries in your ledger.
  • Processing fees, refunds, chargebacks and adjustments booked separately.
  • Orders paid through other gateways, reconciled from their own reports, see PayPal reconciliation.
  • Several stores or currencies in the same workspace.

Shopify as one channel among many

Most brands do not sell through Shopify alone. On Growth and Scale, Shopify sits next to Amazon, Stripe and PayPal in one workspace, each reconciled to the same bank accounts. The ecommerce reconciliation software page shows the full month for a multi-channel store, and Amazon settlement reconciliation covers the marketplace side.

Rules for recurring Shopify lines

Save rules once for items that repeat every month, such as app subscriptions billed through Shopify, shipping label charges or a specific gift card provider. Rules run before AI suggestions and are unlimited on Growth and Scale. More on rules on how automated reconciliation works.

A Shopify payout, broken down

Say a Shopify Payments payout of $6,240 lands in your bank on Tuesday. The payout export shows it covered orders worth $6,700, processing fees of $210, two refunds totaling $190 and a $60 chargeback. Reconciles groups those lines under the payout, confirms they equal the deposit and labels the match "payout batch net of fees". Revenue is booked at $6,700, the $210 goes to fees and the refunds and chargeback reduce revenue, instead of a single $6,240 sales line that hides all three.

Shopify payout reconciliation questions

Reconcile your Shopify payouts

Upload your bank statement and a Shopify payout export. You see the first matched payouts before you create an account. See pricing for plan limits.

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