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I appreciate what you've done so far, @Ballentine. I'm here to help you get the best help with finding overall concern in QuickBooks Online.
I recommend contacting our QuickBooks Online live support so they can take a look at your QBO account and can properly assist you with the correct recording of refund and deposits.
Here's how:
If you send an invoice to your customer and it automatically records after they paid, this could be due to the Automatic Apply Credit feature turned on. However, this could also be caused by lots of factors.
Since you're dealing with journal entries already, I also recommend consulting with a professional accountant. This way, they can help you record everything correctly and keep your books accurate. You can check out this article to look for an expert near you: Find a QuickBooks Certified ProAdvisor tool.
Additionally, you can check out the deposit speeds in QuickBooks Payments to learn when the payments are being deposited to your account.
Please don't hesitate to reply if you need further concerns with QBO. I'm here to assist you any time.