Giorgi MazmishviliShopify app developer

E-commerce accounting

How to reconcile Shopify Payments payouts with orders

Why a Shopify Payments payout rarely matches one day's sales, what it contains, and how to match it to the bank deposit and your books.

By Giorgi MazmishviliPublished 5 min read

A Shopify Payments payout is a batch of transactions, not a day of sales. It nets charges against refunds, fees, chargebacks and adjustments, so it rarely equals one day's sales. To reconcile, export each payout, check it adds up to the deposit, and book gross amounts, not the net deposit.

Why a payout doesn't match a day's sales

Three things move money between days:

  • Settlement time. Funds are paid out a set number of business days after capture. In Germany the minimum is 3 business days, not counting weekends and holidays.
  • Batching. You choose a daily, weekly or monthly payout schedule. Payments captured on Friday, Saturday and Sunday are sent together as one payout.
  • Capture time, not order time. Shopify records capture time in UTC. If you capture manually, for example at fulfilment, the clock starts then.

Refunds and chargebacks can settle faster than charges, so one payout can mix this week's refunds with last week's sales.

What is in a payout, and how to book it

The last column is a common approach. Agree the exact accounts with your accountant.

Transaction What it is How to book it
Charge A customer payment for an order Gross sales and VAT, taken from the order
Fee Shopify Payments processing fee Payment fees (expense)
Refund Money returned to a customer Reduce sales and VAT
Chargeback A disputed payment taken back Chargeback loss, or reverse the sale
Chargeback reversal Money returned after you win a dispute Reverse the chargeback entry
Adjustment Other items, such as chargeback fees Book by what the line says
Reserve and release Funds held back, then released Money Shopify owes you

VAT on fees: in the EU (except Ireland) and the UK, Shopify charges its fees with 0% VAT under reverse charge. You record the VAT on the fees yourself in your VAT return.

What is not in the payout

  • Other payment providers. PayPal Express Checkout, Amazon Pay and similar providers pay you directly. PayPal Wallet goes through Shopify Payments only in France and the United States.
  • Manual payment methods, such as bank transfer or cash on delivery.
  • Your Shopify bill for plan and apps. It is charged to your billing payment method. Book it from the invoice.
  • Tax as a separate line. A charge includes VAT, and the export has no tax column. Take the tax split from your orders.

Reconcile one payout, step by step

Export the payout

  1. In your Shopify admin, go to Finance → Payouts.
  2. Click the payout date.
  3. Click the payout you want to reconcile.
  4. Note the payout ID, amount and transfer reference number.
  5. Click the Export icon in the payout details.
  6. Click Export payout transactions.

In the original payouts view, click Export, then Export payout transactions.

The CSV has these columns: Transaction Date, Type, Order, Card Brand, Card Source, Payout Status, Payout Date, Available On, Amount, Fee, Net.

Check the totals

  1. Open the CSV in a spreadsheet.
  2. Group the rows by Type.
  3. Add up Amount, Fee and Net for each type.
  4. Check that the total of Net equals the payout amount.

Match the bank deposit

  1. Find a deposit with the same amount, 1 to 3 business days after the payout date.
  2. Compare the bank reference with the transfer reference number. Not all banks show it.
  3. Mark the payout as matched.

Deposited means the payout left Shopify, not that it reached your account.

Book it

  1. Create a clearing account, for example "Shopify Payments clearing".
  2. Book gross sales and VAT from Shopify Payments orders to it.
  3. Book fees, refunds and chargebacks from the CSV against it.
  4. Book the bank deposit as a transfer from clearing to bank.
  5. At month end, check that the clearing balance equals transactions not paid out yet.

Don't book the deposit as sales. That hides your fees, refunds and VAT.

Accounting integrations can import payouts automatically. They use the same logic, so check one payout by hand first.

For month-end, go to Finance → Documents → Shopify Payments activity report and click Export to PDF. It summarises balance activity, fees and payouts for a date range. It has a 3-day data delay and is not a revenue statement.

Worked example

A hypothetical weekly payout in euros:

Line Amount (EUR)
Charges, 32 orders 2,400.00
Refunds, 2 orders −150.00
Processing fees −72.30
Chargeback −89.00
Adjustment: chargeback fee −15.00
Payout 2,073.70

2,400.00 − 150.00 − 72.30 − 89.00 − 15.00 = 2,073.70.

In the books, sales stay at 2,400.00. Fees are 87.30 (72.30 + 15.00). Check: 2,073.70 + 87.30 + 150.00 + 89.00 = 2,400.00.

Common sticking points

  • Refunds in a later payout. A refund is deducted from the next available payout, not the one with the original charge. Match it by order number.
  • Late chargebacks. A chargeback can arrive long after the sale and is deducted from your next available payout. If you win, the money returns as a separate line. Depending on your country, the fee might be refunded too.
  • Several currencies. Each payout currency has its own payouts and activity report. Sales in a currency without its own payout account are converted, and a fee can apply. Reconcile one currency at a time.
  • Negative payouts. If refunds and chargebacks exceed sales, the balance goes negative. In regions that debit negative balances, Shopify takes the money from your bank (status Withdrawn). Book it as a negative payout.
  • Holds and reserves. An account review can hold all or part of a payout. A reserve holds back part of your funds for a time. Book reserved money as owed to you, not as a loss.

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