Some QuickBooks Payments deposits weren't automatically recorded. After you receive the funds in your account, record them manually as a Bank Deposit.Take Action

I'm here to help you resolve the error message about bank deposit, @apeterson3.

QuickBooks will automatically record if there is a matching sales receipt or payment on an invoice. Otherwise, you will get an error “Some QuickBooks Payments deposits weren't automatically recorded. After you receive the funds in your account, record them manually as a Bank Deposit.”

Payments processed in the Merchant Service Center, the deposits won't import into QuickBooks Online. You'll need to add them manually. To avoid doing this, you can process the payments in QuickBooks Online.

I'll show you how to match and record your deposit.

Here's how to find out which payments are in the deposit:

1. Go to Settings ⚙, then select Account and settings.
2. Select Payments, then Manage Account.
3. Choose Activity & Reports, then Deposits.
4. Click the latest deposit to see the individual payments.

To match your total deposits, record all the missing transactions in QuickBooks Online, follow the steps below.

1. Go to + New, then select Bank deposit.
2. Select the QuickBooks Payments section.
3. Match the payments in the list with the payments in the Merchant Service Center report.
4. Click Save, then Close.

I'm adding this article for future reference in running reports in QuickBooks Online: Run reports in QuickBooks Online.

Let me know if you need further assistance about bank deposit in QuickBooks Online. I'm always here to help. Have a great day.