When you send an invoice to a customer, you can enter the tax withheld while recording the payment manually.
Login to your Zoho Books account and click on the Invoices module. Select the desired invoice and click on the Record Payment button.
In the screen that follows, click the checkbox against Tax Deducted? and enter the amount in the Amount Withheld field.
Finally, click on Save to record the payment after withholding the tax amount.