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Directly deactivating a customer with recurring invoice is currently unavailable. Doing so can trigger an error message saying "This customer cannot be deleted because it is used on a recurring template." Let me walk you through alternative procedures to delete the customer on your end.
You have to delete first the recurring invoice that is tied to the customer that you want to delete on the program. I'll show how:
Click the Gear icon ⚙ in the upper right corner.
Under Lists, select Recurring transactions.
Locate the Template Name and select ▼.
Choose Delete from the Action column.
Select Yes to confirm you want to delete the template.
Once done, you can now make the customer inactive which hides from lists and menus. Please know that even if a customer is inactive, all transactions will still be available on reports.
Here's how:
Go to the Sales menu and select the Customers section.
Choose the customer's name to open their profile.
Select the dropdown ▼ next to Edit.
Choose Make inactive. Then confirm by selecting Yes, make inactive.