Filing GST returns is the single most time-sensitive compliance obligation for Indian businesses - miss the GSTR-1 deadline and your customers cannot see your invoices in their GSTR-2A. Miss the GSTR-3B deadline and late fees accrue at Rs 50 per day (Rs 20 for nil returns) plus interest at 18% per annum on the tax unpaid. Zoho Books eliminates the need to manually re-enter data on the GST portal - your transactions flow directly from your accounting software to the GSTN through Zoho's GSP integration.
This guide covers the complete GSTR-1 and GSTR-3B filing process from within Zoho Books - from enabling API access and pushing data to GSTN, through the approval workflow, tax payment, ITC offset, and marking as filed. For the foundational GST configuration, see our Zoho Books GST setup guide.
What Are GSTR-1 and GSTR-3B?
| GSTR-1 (Outward Supplies) | GSTR-3B (Summary Return) |
|---|---|
| Details of all outward supplies (sales invoices, credit notes, debit notes, exports) | Consolidated summary of output tax liability, ITC claimed, and net tax payable |
| Invoice-level detail (B2B) and consolidated (B2C) | Summary figures - no invoice-level detail |
| Due: 11th of following month (monthly); 13th after quarter (QRMP) | Due: 20th of following month; 22nd/24th (QRMP by state) |
| Filed first - forms the basis for recipients' GSTR-2A/2B | Filed after GSTR-1 - includes ITC from GSTR-2B reconciliation |
| Late fee: Rs 50/day (Rs 20 nil) capped at Rs 10,000 | Late fee: Rs 50/day (Rs 20 nil) capped at Rs 10,000 + 18% interest on tax |
For professional GST return filing support, explore our GST return filing services. For Zoho Books setup and ongoing management, see our Zoho Books accounting services.
Key Terms You Should Know
- API Access: Application Programming Interface access enabled on the GST portal that allows Zoho Books to communicate with GSTN. Must be enabled once - Settings → My Profile → Manage API Access on gst.gov.in.
- Push to GSTN: The action of sending transaction data from Zoho Books to the GST portal. This does not file the return - it only uploads the data for review.
- OTP Authentication: One-Time Password sent to your GST-registered mobile/email when pushing data. Required for security verification.
- Unpushed Transactions: Transactions in Zoho Books that have not yet been sent to GSTN. These must be pushed before filing.
- ITC Offset: Using Input Tax Credit to pay output GST liability. After filing GSTR-3B, Zoho Books creates an automatic journal for ITC offset.
- QRMP Scheme: Quarterly Return Monthly Payment - businesses under Rs 5 crore turnover file GSTR-1 and GSTR-3B quarterly but pay tax monthly using a challan.
- Documents Issued: Section in GSTR-1 where you declare the invoice number series used during the period - must be entered manually before pushing.
One-Time Prerequisite: Enable API Access on the GST Portal
Before you can file any return from Zoho Books, you must enable API access on the GST portal. This is a one-time setup:
- Log in to gst.gov.in with your GSTIN credentials.
- Click your profile name (top right) → My Profile.
- Click 'Manage API Access' from Quick Links.
- Select 'Yes' under 'Enable API Request' and set the duration (recommended: maximum available).
- Save. API access is now active.
Also verify: In Zoho Books → Settings → Taxes & Compliance → Online Filing Settings - enter your GSTN username and authenticate. This completes the two-way connection. For plan selection, use our pricing calculator - GST filing is available from the Standard plan.
How to File GSTR-1 from Zoho Books: Step-by-Step
- Navigate to GST Filing (left sidebar) → Select the period under GSTR-1.
- Review Unpushed Transactions. Click 'Unpushed Transactions' to see all invoices, credit notes, and debit notes for the period. Verify the Transaction Summary, HSN summary, B2CS (B2C small) summary, and NIL-rated supplies. Cross-check invoice counts and tax totals with your sales reports.
- Enter Documents Issued details. Go to the Documents Issued tab → Click Edit → Enter the invoice number series used during the period (from number, to number, total, cancelled). This is mandatory and must be completed before pushing.
- Enter Aggregate Turnover. When prompted, enter your aggregate turnover for the preceding financial year and (if applicable) April-June turnover. This determines your filing frequency.
- Push to GSTN. Click 'Push to GSTN'. Enter the OTP sent to your registered mobile/email. Click 'Verify and Push'. Zoho Books sends all transaction data to the GST portal. Wait for confirmation - you will receive an email and in-app notification.
- Verify on the GST Portal (recommended). Log in to gst.gov.in → Return Dashboard → GSTR-1 → Review the summary. Verify totals match Zoho Books. This is optional but recommended for the first few filings.
- File the Return. In Zoho Books → GST Filing → GSTR-1 → File Your Return tab → Click 'File' (or 'Submit' on the GST portal). The return is filed and a confirmation ARN is generated.
- Mark as Filed in Zoho Books. If you filed directly on the GST portal instead of through Zoho Books, go back to Zoho Books → GST Filing → GSTR-1 → Click 'Mark as Filed'. This updates the status and prevents re-filing.
Pre-GSTR-3B Step: Reconcile GSTR-2B
Before filing GSTR-3B, reconcile your GSTR-2B with your purchase register in Zoho Books. This ensures the ITC you claim in GSTR-3B matches the ITC available on the portal. For the detailed reconciliation process, see our bank reconciliation guide which covers the monthly workflow that includes GSTR-2B reconciliation.
- Go to GST Filing → GSTR-2B → Pull data from GSTN (available from 14th of the month).
- Compare with your purchase register - Zoho Books flags matched, partially matched, and missing invoices.
- Resolve mismatches: contact vendors for missing invoices, correct tax rate errors, exclude ineligible ITC.
- Finalise the ITC amount you will claim in GSTR-3B based on reconciled data.
How to File GSTR-3B from Zoho Books: Step-by-Step
- Navigate to GST Filing → GSTR-3B → View Summary.
- Review the GSTR-3B Summary. Zoho Books auto-compiles: Table 3.1 (outward supplies), Table 3.2 (inter-state supplies to unregistered persons), Table 4 (eligible ITC), Table 5 (exempt/nil-rated/non-GST supplies), and Table 6 (payment of tax). Verify each table against your records.
- Push to GSTN. Click 'Push to GSTN' → Enter OTP → Click 'Verify and Push'. The summary data is uploaded to the GST portal.
- Make Tax Payment on the GST Portal. Log in to gst.gov.in → Return Dashboard → GSTR-3B → Preview → Proceed to Payment. Offset your tax liability using ITC (IGST first, then CGST, then SGST). Pay the balance via Electronic Cash Ledger. Generate the payment challan.
- File on the GST Portal. After payment, file GSTR-3B on the portal using DSC or EVC. The return is filed and ARN is generated.
- Record the Payment in Zoho Books. Go to Zoho Books → GST Filing → GSTR-3B → GST Payment tab → Click 'Record Payment'. Enter challan details. If you paid via ICICI Bank integration, this is recorded automatically.
- Mark as Filed in Zoho Books. Click 'Mark as Filed'. Zoho Books automatically creates a journal entry for ITC offset - debiting GST Payable and crediting GST Input accounts.
Setting Up the Filing Approval Workflow
Navigation: Settings → GST Filing → Enable Approval Process
The approval workflow ensures that no return is filed without review. When enabled, users must click 'Submit for Approval' after pushing data to GSTN. The designated approver (up to 5 approvers - typically the CA or senior accountant) receives a notification, reviews the summary, and either approves or rejects with reasons. Only approved returns can be filed. This prevents accidental filing of incorrect data - once filed, GSTR-1 data cannot be recalled (only amended in the next period).
GSTR-1 vs GSTR-3B Filing Workflow in Zoho Books: Key Differences
| Step | GSTR-1 | GSTR-3B |
|---|---|---|
| Data Source | Invoice-level detail (all outward supplies) | Summary of output liability + ITC claimed |
| Pre-Requisite | All invoices/CNs finalised, Documents Issued entered | GSTR-1 filed + GSTR-2B reconciled (recommended) |
| Push to GSTN | Pushes all transaction details | Pushes summary figures only |
| Tax Payment | Not required - GSTR-1 is informational | Required - offset ITC + pay balance via ECL |
| Filing Location | Can file entirely from Zoho Books OR from GST portal | Push from Zoho Books → Pay and file on GST portal → Mark as filed in Zoho Books |
| Post-Filing Action | Mark as Filed (if filed on portal separately) | Record payment + Mark as Filed → Auto ITC offset journal |
| Amendment | Errors amended in next period's GSTR-1 (Section 9A/9C) | Cannot be amended - corrections in subsequent period |
Common GSTR Filing Mistakes in Zoho Books
Mistake 1: Not entering Documents Issued before pushing GSTR-1. The Documents Issued section is mandatory. If you push without completing it, the GSTR-1 on the portal will have incomplete data. Always enter the invoice series (from, to, total, cancelled) before pushing.
Mistake 2: Filing GSTR-3B without reconciling GSTR-2B. If you claim ITC that is not available in GSTR-2B, you may receive a DRC-01C notice requiring you to explain the mismatch or reverse the excess ITC with interest. Reconcile GSTR-2B between the 14th and 18th before filing GSTR-3B by the 20th.
Mistake 3: Pushing data with unresolved errors. Zoho Books flags 'Failed' transactions during push - these are invoices with missing GSTINs, invalid HSN codes, or wrong tax rates. Do not ignore failures. Fix the transactions and re-push before filing.
Mistake 4: Not recording the GST payment after GSTR-3B filing. After paying tax on the GST portal and filing GSTR-3B, you must record the payment in Zoho Books (GST Filing → GST Payment → Record Payment). Without this step, your GST Payable liability in Zoho Books remains open and your bank reconciliation will not match.
Mistake 5: Filing from Zoho Books without enabling the approval workflow. Without approval, any user with filing access can accidentally push and file incorrect data. Once GSTR-1 is filed, it cannot be recalled - only amended in the next period. Enable the approval workflow for all organisations. For end-to-end support, explore our Zoho Books accounting services.
Monthly GST Filing Calendar in Zoho Books
| By Date | Action | Zoho Books Path |
|---|---|---|
| 1st-5th | Complete bank reconciliation for previous month | Banking → Reconcile |
| 5th-8th | Finalise all invoices, credit notes. Enter Documents Issued | Sales → Invoices; GST Filing → GSTR-1 → Documents Issued |
| 8th-10th | Push GSTR-1 to GSTN and verify summary | GST Filing → GSTR-1 → Push to GSTN |
| 11th | File GSTR-1 (due date for monthly filers) | GST Filing → GSTR-1 → File Your Return |
| 14th-15th | Pull GSTR-2B from GSTN and reconcile with purchases | GST Filing → GSTR-2B → Pull from GSTN |
| 15th-18th | Resolve GSTR-2B mismatches - vendor follow-up, corrections | Reports → GST Mismatch Report |
| 18th-19th | Push GSTR-3B to GSTN and verify summary | GST Filing → GSTR-3B → Push to GSTN |
| 19th-20th | Pay GST on portal. File GSTR-3B. Record payment in Zoho Books. Mark as Filed | gst.gov.in → Payment; Zoho Books → GST Filing → Record Payment |
| 20th-25th | Lock the accounting period. Generate and archive GST reports | Settings → Closing Books; Reports → GST Reports |
QRMP Scheme: Quarterly Filing from Zoho Books
If your business has aggregate turnover up to Rs 5 crore, you can opt for the QRMP (Quarterly Return Monthly Payment) scheme. Under QRMP, GSTR-1 and GSTR-3B are filed quarterly instead of monthly. However, tax must be paid monthly using a challan (PMT-06) by the 25th of the following month.
In Zoho Books, set your filing frequency to 'Quarterly' in Online Filing Settings. Zoho Books will compile transactions for the full quarter. During the two non-filing months, pay tax using the fixed sum method (35% of the previous quarter's tax) or the self-assessment method. Record these monthly payments in Zoho Books under GST Payments.
Note: Even under QRMP, you must use the Invoice Furnishing Facility (IFF) to upload B2B invoices for the first two months of the quarter by the 13th of the following month. This allows your B2B customers to see your invoices in their GSTR-2B for monthly ITC claims. Zoho Books supports IFF upload.
Key Takeaways
Filing GSTR-1 and GSTR-3B from Zoho Books requires a one-time API access enablement on the GST portal and Online Filing Settings configuration in Zoho Books - after which all returns can be pushed, reviewed, and filed without leaving the accounting software.
GSTR-1 is filed first (by the 11th) with invoice-level detail. GSTR-3B is filed second (by the 20th) with summary figures including ITC. Between the two, GSTR-2B reconciliation (14th-18th) ensures ITC claimed in GSTR-3B matches ITC available from vendors' filings.
The filing approval workflow prevents accidental filing by requiring CA/senior accountant review before submission - critical because filed GSTR-1 data cannot be recalled, only amended in the next period.
After filing GSTR-3B, three actions must be completed in Zoho Books: record the GST payment (challan details), mark the return as filed (triggers status update), and verify the auto-created ITC offset journal (GST Payable debited, GST Input credited).
QRMP scheme businesses file quarterly but must pay monthly by the 25th and use the Invoice Furnishing Facility (IFF) to upload B2B invoices for the non-filing months - Zoho Books supports both workflows.
Need Help Filing GST Returns from Zoho Books?
Filing GSTR-1 and GSTR-3B from Zoho Books requires correct GST configuration, complete transaction data, Documents Issued entry, GSTR-2B reconciliation, and coordination between Zoho Books and the GST portal for payment and filing.
Explore our Zoho Books accounting services for CA-managed monthly GST return filing, GSTR-2B reconciliation, and ongoing compliance support.
For queries, reach out at +91 945 945 6700 or WhatsApp us directly.
