Recently two of my invoices show that they are still due but I received emails saying they were paid and I see the money in my bank?

If your customer paid directly through an external bank transfer instead of using the invoice payment link, QuickBooks Self-Employed cannot automatically match the deposit to your open invoice. However, you can manually mark the invoice as paid.

Follow these steps to update the status:

1. In the left menu, choose Invoices.
2. Locate the invoice and select the small arrow ▼ icon in the Action column.
3. Select Mark as paid.

If your customer used the payment link on the invoice, a temporary system sync delay is likely causing this issue. Intuit Merchant Services sends a payment confirmation email as soon as the card or transfer processes, but the status inside QuickBooks Self-Employed may take a short time to update.

If you have other questions, you can reply to this thread.