I assume the deposit came in first before the invoice, so you'll need to record that first and then apply it as payment to the invoice. Here's an article showing the complete details on how to handle customer prepayments in QBO: Record a retainer or deposit.
Let me know if you have any other questions in mind. Take care and have a good one!
I recognize the advantage of having this option inside QuickBooks Online (QBO). Upon checking here on my end, the feature you're trying to access is unable. If you wish to have this inside QBO, I'd recommend sending a feature request to our Product Development Team. I'll input the steps below to get you going.
Access your QuickBooks Online company.
On the top right-corner, click the Gear icon.
Below the Profile column, select Send Feedback.
Enter a brief description of your feature request.
@SnawDun, if you have any additional QuickBooks-related queries, feel free to leave a comment below. I'll be here to help you sort it out. Stay safe, and have a good one!
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