If the invoices were created in Zoho Books, and your client pays by clicking on the Stripe payment link (available on the invoice), then it will be recorded as a Customer Payment.
If you receive a payment in Stripe for a non-Zoho Books transaction, then it will be recorded as a “Sales Without Invoice” transaction. In that case, please do not create an invoice or record a payment to it, as it will double up the values. Instead, delete the sales without invoice transaction and then create the invoice and manually record the payment for it.
Click here to learn more about integrating Stripe with Zoho Books.
and GST filing.