Shopify Payouts Explained: Why Your Bank Never Shows Your Sales
Your Shopify dashboard says £8,400 of sales this week. Your bank shows three payments adding up to £7,650. Shopify has not lost your money. The difference is in the payouts.
How Shopify pays you
If you use Shopify Payments, customer payments are collected by Shopify and paid to your bank in batches, called payouts. Before paying, Shopify deducts:
- Card processing fees on each order
- Refunds you have given to customers
- Chargebacks, where a customer has disputed a payment, and any dispute fees
- Adjustments, such as fee corrections
Your Shopify subscription and app charges are usually billed separately, not taken from the payout.
Payments taken through PayPal, Klarna, Amazon Pay or other gateways do not go through Shopify Payments at all. Each gateway pays you separately, with its own fees and timing.
The mistake that causes most of the problems
Many sellers record each Shopify bank receipt as sales. The result:
- Sales are understated, because fees and refunds have already been taken off
- Card fees never appear as a cost, so margins look odd
- VAT is calculated on the wrong figure
- Sales through PayPal and other gateways can be missed or counted twice
The right way: a clearing account
The reliable method is to treat Shopify as a separate account that money passes through:
- Record the full sales, shipping and VAT from Shopify’s sales reports into a Shopify clearing account.
- Record fees, refunds and chargebacks against the same clearing account.
- When the payout reaches your bank, record it as a transfer from the clearing account, not as income.
If everything is recorded properly, the clearing account comes back to the amount Shopify still owes you, usually the payouts in transit. If it keeps drifting, something is missing.
Each payment gateway gets its own clearing account, so PayPal is reconciled in the same way.
Tools that help
Connectors such as A2X or Link My Books summarise each payout and post it to Xero or QuickBooks using this method. They save a lot of time, but they depend on being set up correctly. The account and VAT mappings decide where every figure ends up, and an error is repeated on every payout.
Checks worth doing each month
- Does the Shopify clearing account agree with what Shopify says is still to be paid?
- Do total sales in your accounts agree with Shopify’s sales report for the month?
- Are card fees a stable percentage of sales?
- Have refunds and chargebacks increased, and why?
- Is every gateway, including PayPal, accounted for?
Selling on Amazon too?
The same principle applies to Amazon, where the settlement report plays the role of the payout report. Each channel gets its own clearing account, so you can see sales, fees and margin for each one separately. Our free Amazon settlement checker breaks down any Amazon settlement in a few seconds.
If your Shopify sales have been recorded from bank receipts, or your clearing accounts no longer make sense, book a consultation and we can set it up properly.
