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Welcome and thanks for reaching out to the Community, @jonathan-storyla.
We can check the transaction history in the Merchant Services Center to identify what invoice payment you'll include when creating Bank Deposit in QuickBooks Online (QBO) for matching.
From there, you can just base the matching of payment from the customer's name in the Merchant.
For more information about solving QuickBooks Payments deposit issues, I suggest checking out this article: Fix QuickBooks Payment deposits that don't match your bank statement.
Please let me know if you have any other issues or concerns in the comment section below. I'm more than willing to help. Enjoy the rest of the day!
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Great. Thank you for your help. :)