GST and e-invoicing setup in Zoho Books: a practical guide

In the organisation profile, set the business name, address, financial year and currency. Then open GST settings in Settings and mark the organisation as GST registered. Enter the GSTIN. Zoho Books asks for the registration date and the GST treatment, such as regular registration or composition scheme. Pick the one that matches your registration certificate. Getting this wrong changes the tax shown on every invoice.

If you have more than one GST registration (for example, in two states), plan this before importing contacts and items. Each registration has its own GSTIN, place of supply and return. Zoho Books supports multiple registrations through branches. Keep the structure simple and agree it with the CA.

Create tax rates for the slabs you use. Since 22 September 2025 most supplies are at 5% or 18%, with 40% for a short list of specified goods, plus nil-rated and exempt supplies. Invoices for earlier periods may still need 12% and 28%, so keep those rates if you bring history. Zoho Books treats intra-state supply as CGST plus SGST and inter-state supply as IGST, based on place of supply. You do not create separate rates for each.

Set HSN or SAC code and the tax rate on each item. Mistakes here are the most common source of return errors. A wrong rate on an item repeats on every invoice. GSTR-1 asks for HSN summaries with a minimum number of digits that depends on your turnover, so enter the full code. Check the current digit requirement on the GST portal.

For every contact choose the right GST treatment: registered business (regular), registered business (composition), unregistered, consumer, overseas, SEZ, or deemed export. Enter the GSTIN for registered ones and set the place of supply.

This drives the tax on the invoice, the section in GSTR-1 where it appears, and for vendors, whether input credit is available. A composition vendor, for instance, cannot pass on credit, so bills from them should not show tax as claimable.

E-invoicing means each B2B invoice is registered with the government Invoice Registration Portal (IRP), which returns an IRN (Invoice Reference Number) and a QR code. Zoho Books can connect to the IRP and push invoices for you.

Who must do it? The rule is based on aggregate turnover under a PAN. As of 2026 the limit most sources quote is ₹5 crore in any financial year from 2017-18 onwards, as set in Notification 10/2023-Central Tax. Once crossed, it applies even if turnover later falls. Some categories are exempt. Please check the current position on the e-invoice portal or with your CA before relying on this, since limits have changed several times. Separately, taxpayers above a higher turnover limit must report invoices to the IRP within 30 days of the invoice date. Ask your CA whether that applies to you.

What it covers: B2B, supplies to government and exports. B2C invoices do not need an IRN.

To set it up, register on the IRP portal if you have not, using your GSTIN and registered mobile number to create a username and password. Then, in Zoho Books, turn on e-invoicing under Settings. Zoho's release notes describe the path as Settings, then Preferences, then e-Invoicing, but screens are reorganised from time to time, so look under GST settings too. Connect with your IRP credentials. Zoho's help documents the IRP registration and the connection steps.

After this, when you create an invoice you push it to the IRP. The status changes to pushed, and the IRN and QR code are stored on the invoice. You can push many together, and recurring invoices can be set to push automatically. Cancelling an e-invoice is possible within a short window on the IRP (24 hours is the usual limit). After that, issue a credit note instead.

An e-way bill is needed for moving goods above ₹50,000 in value, with exceptions, and some states have different limits for movement within the state. Zoho Books can generate an e-way bill from an invoice once your e-way bill portal credentials are connected. You enter vehicle number or transporter ID, distance and transport mode.

If you are required to use e-invoicing, the IRP can pass the data for the e-way bill so it is generated along with the invoice. Test this with a real consignment before you rely on it. Do not discover a mismatch of vehicle or distance at the dispatch gate.

Run these tests on real documents.

1. A B2B invoice within the state, to a regular GST customer, with items at two different rates.
2. A B2B invoice outside the state, to check IGST.
3. A sale to an unregistered customer.
4. An export or SEZ invoice, if you have them.
5. A credit note against an earlier invoice.
6. A purchase bill from a registered vendor, one from a composition vendor, and one under reverse charge.
7. An e-invoice push, then check that the IRN and QR show on the printed invoice.
8. An e-way bill from an invoice.

Use the first live month to compare. The GSTR-1 data from Zoho Books should agree with your sales register, and the input credit on purchases should agree with GSTR-2B for the month. Differences usually trace to a wrong treatment on a contact or a missing bill.

Zoho Books prepares data for GSTR-1 and GSTR-3B. For monthly filers the due dates are generally the 11th and the 20th of the next month, subject to notifications and the QRMP scheme if you opted in. Your CA reviews and files. Many businesses file from Zoho Books directly through GST portal integration, and some CAs prefer to export the data and file themselves. Both work. Agree the process before the first due date.

For a sense of how this works for a high-volume seller, see the D2C brand case study, where GST data reaches the CA by the 8th. For how an implementation with e-invoicing and e-way bills went live in four weeks, read the packaging trader case study. If you are weighing the move itself, see Tally vs Zoho Books.