Why your Shopify payout doesn't match your sales (2026): every deduction explained

Updated 10 October 2026 · 7 min read

A Shopify Payments payout is never equal to the sales of the same day. It is the sum of the transactions that became available in that pay period, minus processing fees (including any currency-conversion fee), minus refunds of orders from any earlier date, minus chargebacks and their fee, minus reserves and adjustments, and it excludes every order paid through PayPal, Klarna, gift cards or manual methods. Below is each deduction, where it appears in the transactions export, and how to check it.

The ten reasons a payout is lower than sales

1. Processing fees, including the FX fee you can't see

Every charge row carries a positive Fee, and Net = Amount − Fee. Your rate depends on your plan; Shopify's help page says you "pay the credit card rate, but you don't pay a transaction fee" when using Shopify Payments (Viewing your payout fees).

If the order was paid in a currency other than your payout currency, the currency-conversion fee is added on top: 1.5% in the United States and 2% in all other regions (Currency conversion fees). The export does not split it out. The Fee column is one number that contains processing rate plus conversion fee, and there is no exchange-rate column. That is why fees on international orders look "too high" when you check them against your domestic rate.

In Switzerland, the EU, Australia and Singapore, tax is added to processing fees; the UK and most of the EU apply a 0% reverse charge instead (same page). Taxed fees can appear as separate adjustment rows.

2. Refunds of orders from an earlier period

Refunds are deducted from the next available payout, regardless of when the original order was sold. A March payout can carry a refund for a January order. Two facts matter for reconciliation:

• "The original credit card transaction fee isn't refunded to you when issuing a refund" (Shopify Payments refunds). So the refund row has a negative Amount and usually a Fee of 0; you lose the original fee.
• If the balance can't cover the refund, in most countries "the balance required for the refund is debited from your bank account" on a day outside the payout schedule. In other countries it is deducted from subsequent payouts.

In the orders export there is no refund line and no refund date, only a cumulative Refunded Amount. The refund date exists only in the transactions export, so that is the file to use.

3. Chargebacks and the chargeback fee

When a dispute is opened, "the disputed amount and chargeback fee are withdrawn immediately." If you win, both are returned (Chargeback process). Fees by country:

In the export, the dispute appears as a dispute (or chargeback) row referencing the original order number, and a win appears later as a dispute_reversal row. The two can sit in different payouts, months apart.

4. Reserves

A reserve is set after a risk assessment and is either a fixed amount (Shopify's example: $1,000 for 120 days) or a percentage of each transaction (example: 10%). In the payout it shows as "negative transactions" for the portion held and "positive transactions" when funds are released (Reserves). A release can arrive as one bulk positive line. Reserve rows have no Order value.

5. Adjustments

The "lower or missing payouts" page lists adjustments that "could either increase or decrease the final amount", including chargeback fees, Shopify Protect, and tax adjustments (Lower or missing payouts). Shopify Capital remittances also come out of the balance. In the CSV these are adjustment rows with an empty Order field, so they will never match an order and must be booked on their own.

6. Gift cards, PayPal, Klarna and manual payments

Shopify Payments only pays out money it processed. An order paid 100% by gift card generates no transaction row. An order paid partly by gift card shows a charge for the card portion only. PayPal, Klarna, Shop Pay Installments (settled by the provider) and manual/bank-transfer orders are absent from the export and arrive in your bank account on their own schedules.

In the orders export, the Payment Method column shows shopify_payments, paypal, manual, gift_card, or combinations joined with + . Any order whose method does not include shopify_payments should be excluded before you compare sales to payouts. A reconciliation statement that lists these orders in a "settled outside Shopify Payments" bucket, which is what the payout statement tool at Shopify payout statements does from the two CSVs, removes the largest single source of "my payout is 15% below sales" questions.

7. Timing: Available On versus Payout Date

Settlement time is "the amount of time between when a customer's payment is captured and those funds are available to be paid out." It counts business days only, and Friday-to-Sunday transactions "are grouped and sent together as one payout" (Payout timing). Published settlement times:

After the payout is sent, banks take a further 1 to 3 business days to show the deposit. So a sale on Transaction Date 2026-03-05 may have Available On 2026-03-10 and Payout Date 2026-03-10, with the money in the bank on 2026-03-12. Comparing March sales to March payouts will always leave the last few days of the month "missing"; they are pending or in_transit, not lost.

Your payout schedule (daily, weekly on a chosen day, or monthly) is set under Settings > Payments > Manage > Payouts (Schedule payouts). A weekly schedule means one payout contains up to seven days of available transactions plus every refund and dispute that landed in between.

8. Multi-currency stores

Amount, Fee and Net are in the payout currency (Currency column). Presentment Amount and Presentment Currency are what the customer paid. Shopify recommends refunding "the full amount that the customer paid in their local currency", which means "you might lose or gain money due to currency conversions" because the refund uses the rate on the refund date (Exchange rates). A EUR 100 order refunded in full can come back as a negative Amount that differs from the original positive one by several dollars. Stores with more than one payout currency receive separate payouts per currency; reconcile each currency on its own.

How to check a payout in five minutes

1. Finance > Payouts > click the payout date > Export icon > Export payout transactions. The CSV is emailed (View payout details).
2. Sum Amount on charge rows: that is gross card sales in the payout.
3. Sum Fee on all rows: that is your fee expense.
4. Sum Amount on refund, dispute, reserve, adjustment rows separately.
5. Check that Σ Net equals the payout total on the Payouts page.
6. Join Order to the orders export Name to find which orders are inside; everything left over in the orders export is either not yet paid out or settled elsewhere.

FAQ

Why is the fee on some orders higher than my advertised rate? Those orders were paid in a currency other than your payout currency. The 1.5% (US) or 2% (elsewhere) conversion fee is added inside the same Fee figure, with no separate column.

Do I get the processing fee back when I refund an order? No. Shopify's refunds page states the original transaction fee is not refunded. Expect a refund row with the negative amount and a Fee of 0.

My payout is negative. What happened? Refunds and chargebacks in the period exceeded charges. Depending on your country, Shopify either debits your bank account or carries the negative balance into subsequent payouts.

Why don't PayPal orders show in the payout? Shopify Payments pays out only what it processed. PayPal, Klarna and manual payments settle through their own providers and never appear in the Shopify Payments transactions export.

Which column tells me when the money was actually sent? Payout Date. Available On is when the funds finished settling; Transaction Date is when the card was captured.