Shopify payout reconciliation: match payouts to bank deposits

• All payouts for a date range: Shopify admin > Finance > Payouts > View transactions > Export > Items by date. Pick CSV, then Export items.
• One payout: Finance > Payouts, click the payout date and the payout, then the Export icon > Export payout transactions.
• Your bank: download the checking account activity as CSV for the same dates, plus a week.

Shopify emails the CSV to you and the store owner. The columns are Transaction Date, Type, Order, Card Brand, Card Source, Payout Status, Payout Date, Available On, Amount, Fee and Net. The tool finds those headers on its own.

Every row with the same Payout Date belongs to one payout. The tool adds up each row by its Type:

• Sales: charge rows (Amount)
• Refunds: refund rows (Amount)
• Fees: the Fee column on every row
• Chargebacks: dispute rows
• Adjustments and reserves: everything else

Sales + refunds + chargebacks + adjustments - fees = the payout. That total should equal one bank deposit.

It then looks for a bank deposit for the same amount, to the cent, from one day before to five days after the payout date. You can change the five.

• Amount differs: no exact match, so it shows the nearest unused deposit in that window and the gap.
• Payout failed or Not sent yet: taken from the Payout Status column.
• Not found in bank: the bank file covers the dates, but no deposit fits.

• Timing. Shopify says a payout typically takes 1 to 3 business days to arrive. A “Deposited” payout was sent, but the funds may not be in your account yet.
• Failed payouts. “Failed” means your bank couldn’t process the payout. Follow the prompts in Finance > Payouts.
• Bank reference. Payout details show a bank reference number when one is available. Copy it and give it to your bank to trace the payout.
• Other processors. Deposits from PayPal or another processor have no Shopify Payments payout, so they land in the “no matching payout” list.

If your Shopify sales reach QuickBooks Online through an app, our field guide on Shopify orders not syncing to QuickBooks Online covers where that link breaks.

Record one bank deposit per payout, so it equals the line on your bank statement:

1. Select + Create > Bank Deposit and choose the checking account.
2. Tick each Shopify sale that is part of the payout.
3. Under Add funds to this deposit, add the fees as a negative amount to Bank Charges & Fees.
4. Check the total equals the bank amount, then Save and close.

Intuit’s guide says to leave the original transactions as they are and add the fee as its own line. To see what those fees do to your margin per order, read your real Shopify margin after fees, refunds and shipping.