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Recording QuickBooks Payments bank deposits FAQs

Get answers to frequently asked questions about recording merchant service deposits.

Here are some frequently asked questions about automatically recording and matching merchant service deposits in QuickBooks Desktop.

I can’t find my transactions in the merchant service deposit

Here’s where to look for transactions in your merchant service deposit:

  • Add payments to record tab: Select any batch that has a status of Add payments to record, then expand the batch to see the transactions. To record them, select the payment to record under the batch, then select Add payment.
  • Recorded tab: These are transactions that have been matched with invoices and recorded. Select any of the batches to expand them, then look for the transactions.
  • Pending for deposit tab: These are transactions are still pending and usually funded in 2-3 business days.

Fix "In order to make a deposit, you need a valid expense account" error

This means the user you're signed in as doesn't have the right permissions. Don't worry.

Either switch to an admin user, or sign in as an admin and give the user permission to create and print checks. They also need permission to create, modify, and view account balances on the chart of accounts.

Give them permission for:


  • Create
  • Print

Chart of Accounts

  • Create
  • Modify
  • View Account Balance

Can I record my deposits and fees separately if I use automatic match and record of payments?

If you’re using automatic match and record of transactions, you’re not able to record deposits and fees separately. We record both the deposits and fees together, and you can find them in your deposits and fees account that’s set up in your deposit settings.

I see duplicate entries when I record fees, what do I do?

If you’re seeing duplicate fees being recorded, this is usually because the memo field in your chart of accounts was edited. We recommend not editing this field to avoid duplicate fees being recorded.

I’m having an issue while adding payments to my transactions, what do I do?

If you’re unable to add payments to a transaction, you can dismiss them. You’ll need to add these transactions manually, then you can record the payments.

This can happen if there’s an overpayment on the invoice or the invoice was marked paid without adding the payment from your merchant service deposit.

For eInvoice transactions you’ve added manually, we recommend you delete the recorded entries and add the payments from your merchant service deposit.

How do I add payments for an eInvoice?

We recommend adding payments for an eInvoice through merchant service deposits. This way, you’ll have the right balances if your customer makes partial payments.

How do I turn off automatic matching and recording of payments?

If you’d like to manually match and record deposits and fees, you need to turn off automatic reconciliation first. Here’s how.

  1. Go to Banking, then select Record Merchant Service Deposits.
  2. Go to Deposit Settings, then select the Auto match is record is turned on toggle.
  3. Select Save Settings.

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