Most eBay refunds and fees are taken from your seller balance as part of eBay Managed Payments. If your seller balance doesn't cover the cost, eBay will charge your card or bank account on file directly for the shortfall. Link My Books handles these the same way, as explained below.

Yes. When eBay charges your card or bank account on file, eBay include two transactions in the payout report for the period the charge occurred in. The example below is a refund, but a fee shortfall (such as promoted listings) works the same way.

The first transaction is the refund itself, including any refunded eBay fees too:

In this example, the refund minus the fee credits comes to £421.49 which is equal to the amount eBay took from your bank account, see below.

The second transaction is the credit for the funds taken from your bank account:

Importantly this account transfer amount will be allocated to your chosen eBay Dispute Reserved Balances account and tax rate, which is "eBay Dispute Reserved Balances" and "No VAT" if you use our default accounts and tax rates. Additionally, you should review this nominal to ensure all fees have been accounted for correctly before completing the classification process.

Despite its name, the eBay Dispute Reserved Balances account (LMB45) isn't just for disputes. It works as a clearing account for any money moving between eBay and your card or bank outside the normal payout — refunds, disputes and fee shortfalls alike.

The refund or fee itself is accounted for in the invoice/journal Link My Books created for the eBay payout. Still, there are two actions to take to reconcile both the deposit from eBay for that payout and the charge eBay took directly from your card or bank account.

Firstly you will reconcile the amount received into your bank account for the full payout value against the invoice/journal entry created by Link My Books for that payout as normal.

Secondly, to account for the amount eBay charged directly to your card or bank account you will need to create an expense transaction and assign that to your eBay Dispute Reserved Balances account, and ensure that it has the same No VAT tax rate selected (if you use the Link My Books default accounts and tax rates). After creating the expense transaction, manually allocate and reconcile the payment to the "LMB45: eBay Dispute Reserved Balances" nominal in Xero to ensure accuracy.

This will ensure everything is where it should be, all accounted for and both the payout amount and the card or bank charge have been reconciled.

If eBay charged your card or bank account for fees and there's no matching Account Transfer line in the payout, those fees were billed to you directly rather than taken from your payouts, so Link My Books hasn't accounted for them. Enter them as a bill in Xero or QuickBooks against your eBay fees account (LMB44 if you use our default accounts). Check the VAT rate for each fee on your monthly eBay invoice — most are 20% VAT on expenses, but some postage labels are zero rated. See Does Link My Books account for all eBay fees on my monthly invoice?