Thank you for posting here in the Community, @Briana L.

Yes, setting up recurring Annual invoices with Quarterly payments can be done in QuickBooks Desktop. I'd be happy to guide you through the steps.

In QBDT, it's called a memorized transaction. You'll have to enter the invoice first to create a repeating transaction. Here's how:

1. Go to the Customers menu, then select Create Invoices.
2. Select the customer from the drop-down.
3. Enter the sales information.
4. From the Terms drop-down, select Net 90. If you don't have it, click Add New and create a new one.
5. Then, click Memorize.
6. In the Memorize Transactions window, enter the name of the template.
7. Select either Add to my Reminders List if you want to receive a reminder and manually enter the transaction. Or Automate Transaction Enter if you want the system to create it for you.
8. Choose Annually from the How Ofter drop-down, then enter the next date.
9. Fill out the necessary information, like the Number Remaining and Days In Advance To Enter fields.
10. Click OK. Then, Save the invoice.

I'm adding this article for more guidance: Create, edit, or delete memorized transactions. This article will also guide you on how to manage existing memorized transactions.

Just in case you encounter damaged transactions in your QBDT, feel free to read this article for the detailed steps on how to fix it: Fix damaged transactions in QuickBooks Desktop.

Please post a reply below if you have other concerns with your transactions in QuickBooks Desktop. I'll be more than happy to assist you again. Have a great day and take care always.