In Sage Sole Trader, invoices and payments are separate. Marking an invoice as paid doesn’t automatically create a payment.
When using a bank feed, check whether the payment has pulled through as a bank transaction. If it has, just mark the invoice as paid. Don’t create a new transaction.
If the payment isn’t on your bank feed, record it manually. You can create the payment directly when marking the invoice as paid, or from the bank area.
The outcome is the same: one invoice marked as paid, and one payment recorded in your bank.
The invoice now shows as Paid or Part-paid, depending on the amount entered.