You've checked your Shopify dashboard. You've checked Xero. The numbers are different — sometimes by a little, sometimes by enough to be alarming. This is not a bug and it doesn't mean someone has taken your money. It's how Shopify Payments is designed to work.
Why the Numbers Are Always Different
Shopify Payments batches transactions over a rolling period (typically 3-5 business days) and sends a single net payout: gross sales, minus refunds, minus Shopify Payments transaction fees, minus chargebacks, across all orders in that period. The payout period doesn't align with calendar months, your Shopify reporting periods, or anything in Xero.
| What Shopify Shows | What Xero Bank Feed Shows |
|---|---|
| Gross order value (before fees) | Net payout (after fees and refunds) |
| Calendar month sales | Rolling payout period (3-5 days) |
| All payment methods combined | Shopify Payments only |
| Sales at time of order | Cash received at time of payout |
The Four Specific Causes of the Discrepancy
1. Payment processing fees. Shopify deducts transaction fees (2.0%, 1.7%, or 1.5% depending on plan, plus 25p) before paying you. These are silently deducted from each payout — not itemised in the bank feed.
2. Timing differences. An order placed on 28 October might land in a November payout. Shopify's rolling payout window creates a permanent timing difference between when orders happen and when money arrives.
3. Refunds. When you process a refund, Shopify reduces your next payout. Xero sees a reduced payout but doesn't automatically know there was a refund inside it.
4. Multiple payment methods. Shopify Payments only covers card transactions. PayPal, Klarna, or other gateways arrive in separate bank feeds. Your Shopify gross sales figure includes all of them.
The Wrong Way to Reconcile
The most common — and most wrong — approach is matching each bank transaction to a single invoice for the Shopify total revenue figure for the period. This creates a £6,120 invoice matched to a £4,847 bank entry, leaving a £1,273 discrepancy that sits unreconciled forever or gets written off.
The Right Way: A2X or Link My Books
With A2X or Link My Books properly configured, each Shopify payout creates a reconciliation summary in Xero: gross sales, returns deducted, Shopify fees deducted, net payout total — matching exactly to the bank feed entry. Reconciliation is a single click. This is a one-time setup that reduces monthly bookkeeping from hours to ten minutes.
Setting Up the Fix
- Connect A2X or Link My Books to your Shopify account and Xero/QuickBooks
- Configure the nominal code mapping — which Shopify transaction types map to which Xero accounts
- Set the correct tax treatment for each transaction type
- Run a historical import to clean up previous periods
- Reconcile each bank feed entry to the matching payout summary
- Set up the same process for PayPal, Klarna, or any other gateway as a separate integration
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All guides on this site are reviewed for technical accuracy by qualified accountants in our network before publication.