Most small businesses in India do not have a GST problem. They have a calendar problem. The tax itself is arithmetic; the pain comes from doing that arithmetic in a panic on the 19th, from a WhatsApp folder of invoice photographs, against a credit ledger nobody has reconciled since April. Choosing GST software for a small business in India only helps once the rhythm exists, so we start with the rhythm.
Plainly, once: this is general information, not tax or legal advice. Rates, thresholds and due dates change by notification, sometimes at short notice. Verify anything that moves money on the GST portal itself, and put a chartered accountant on anything not routine — a notice, a refund, a registration change, an unclear rate classification, or a year you filed badly.
Three changes that broke the old way of filing
If your process was designed before 2025, it is probably out of date in three specific ways.
The rate structure was rebuilt. Following the 56th GST Council meeting on 3 September 2025 and CBIC notifications issued on 17 September 2025, the structure moved to two principal slabs of 5% and 18%, with 40% for demerit and sin goods such as tobacco, pan masala and online gaming. The 12% and 28% slabs were folded away. Every item master, saved invoice template and recurring bill needed re-rating, and we still meet businesses running HSN-to-rate mappings restored from a 2024 backup.
GSTR-3B stopped being a free-text form. From the July 2025 tax period, the outward liability auto-populated into GSTR-3B from GSTR-1, GSTR-1A and the Invoice Furnishing Facility is hard-locked. You can no longer type a different number into Table 3 because the sales register disagrees. Corrections go through GSTR-1A, filed after GSTR-1 and before GSTR-3B for the same period.
Old returns expire. Returns cannot be filed once three years have passed from their due date, and the portal began enforcing this in 2025. A pending GSTR-3B from four years ago is not a problem you can defer; it closes on its own and leaves the liability behind.
Decide which filing track you are on first
Everything downstream depends on this. There are three tracks.
Composition
Open to most businesses with aggregate turnover up to Rs 1.5 crore (Rs 75 lakh in the north-eastern states and Himachal Pradesh). Tax is a flat share of turnover — broadly 1% for traders and manufacturers, 5% for restaurants not serving alcohol, 6% for other service providers. The trade-off is real: no input tax credit, a bill of supply instead of a tax invoice, and no inter-state outward supply. Filing is light — quarterly CMP-08 and one annual GSTR-4.
QRMP
For regular taxpayers up to Rs 5 crore turnover. You file GSTR-1 and GSTR-3B quarterly but pay monthly through Form PMT-06. In months one and two you may optionally upload B2B invoices through the Invoice Furnishing Facility, capped at Rs 50 lakh a month, so buyers see credit without waiting for the quarter to close. If your customers claim credit, use the IFF; if you sell to consumers, skip it.
Monthly
Everyone above Rs 5 crore, plus anyone under it who chooses it. More work, shorter feedback loop — mismatches surface within weeks rather than at quarter end.
The filing calendar, form by form
| Form | Who files it | Due date | What it covers |
|---|---|---|---|
| GSTR-1 | Monthly filers | 11th of the following month | Outward supplies, invoice-wise for B2B |
| IFF (optional) | QRMP, months 1 and 2 | 13th of the following month | B2B invoices only, up to Rs 50 lakh a month |
| GSTR-1 (quarterly) | QRMP filers | 13th of the month after quarter end | The quarter’s outward supplies |
| GSTR-1A | Any filer, optional | After GSTR-1, before GSTR-3B | Amendments to that period’s outward supplies |
| PMT-06 | QRMP, months 1 and 2 | 25th of the following month | A payment challan, not a return |
| GSTR-2B | Generated, not filed | Draft from the 14th | Static statement of credit available to you |
| GSTR-3B | Monthly filers | 20th of the following month | Summary liability, credit claimed, tax paid |
| GSTR-3B (quarterly) | QRMP filers | 22nd or 24th after quarter end, by state group | As above, for the quarter |
| CMP-08 | Composition | 18th of the month after quarter end | Self-assessed quarterly tax |
| GSTR-4 | Composition | 30 June following the financial year | Annual return |
| GSTR-9 | Turnover above Rs 2 crore | 31 December following the financial year | Annual consolidation |
| GSTR-9C | Turnover above Rs 5 crore | With GSTR-9 | Self-certified reconciliation to audited accounts |
Confirm your state group for the 22nd-versus-24th split, and confirm every date above on the portal before relying on it. Extensions do get notified.
The month, in three blocks
The loop we would run is deliberately front-loaded, because the expensive mistakes all come from compressing the work into the last two days.
Days 1 to 10 — close the previous month
Stop issuing invoices dated into the closed month. Push every sales invoice, credit note and debit note into the books, in sequence, no gaps. Enter every purchase bill, including the ones on the owner’s personal card. Reconcile the bank statement. If e-invoicing applies, confirm each B2B invoice carries a valid IRN — one without it, where required, is not a valid tax invoice and your buyer’s credit will not survive it.
Days 11 to 14 — file outward, then wait
Monthly filers file GSTR-1 by the 11th; QRMP filers upload the IFF by the 13th. Then wait. Draft GSTR-2B becomes available from the 14th and is the only statement that matters for what credit you may claim.
Days 14 to 20 — reconcile, then file
Work the Invoice Management System on the portal. Every inward document your suppliers filed lands there and you accept, reject or mark it pending. Accepted documents flow into GSTR-2B as available credit; rejected ones do not; pending holds them for a later period. Take no action and the document is deemed accepted at GSTR-2B generation — which is exactly how businesses claim credit on an invoice they never received.
Then compare GSTR-2B against your purchase register line by line, and chase gaps by the 17th so a supplier still has time to fix the period. File GSTR-3B by the 20th, paying whatever the credit ledger does not cover. If your outward numbers are wrong, file GSTR-1A first — you cannot fix them inside GSTR-3B any more.
The quarterly and annual rhythm
Quarterly, the additions are modest: pay PMT-06 for the first two months by the 25th, file the quarter’s GSTR-1 by the 13th after quarter end and GSTR-3B on the 22nd or 24th. Use the quarter close to check what monthly filing hides — whether turnover is drifting toward a threshold that changes your obligations, and whether credit in “pending” has aged past usefulness.
Annually, above Rs 2 crore turnover you file GSTR-9 by 31 December of the following financial year; above Rs 5 crore, add the self-certified GSTR-9C. Start it in October — every difference it surfaces is one you were carrying all year without noticing.
What we would pay for, and what we would not
Most single-GSTIN businesses under Rs 5 crore are well served by the cheapest tier that handles their invoice volume. Treat every figure below as an indicative list price at the time of writing, exclusive of GST, and check the vendor’s own pricing page before buying — Indian software pricing changes often and is heavily discounted through resellers.
| Software | Indicative price (excl. GST) | Who it suits | Main limitation |
|---|---|---|---|
| TallyPrime | Silver (1 user) about Rs 22,500 one-time; Gold (multi-user) about Rs 67,500; annual TSS roughly Rs 8,100 and Rs 24,300 | Traders and manufacturers with real inventory, and anyone whose CA works in Tally | Desktop-first; remote access needs setup, and lapsed TSS cuts off statutory updates |
| Zoho Books | Free under Rs 25 lakh revenue (1 user); Standard Rs 899/month, or Rs 749/month billed annually (3 users); Professional Rs 1,799/month (5 users) | Service businesses and agencies wanting bank feeds and filing in one place | Inventory is shallower than Tally or Marg; the free plan caps revenue and users |
| Vyapar | Mobile app free; desktop from around Rs 3,399/year; desktop plus mobile from around Rs 4,010/year | Retail counters, kirana stores and workshops where the owner bills personally | Light on accounting structure and audit trail |
| BUSY | Express edition free; subscriptions around Rs 5,000, Rs 8,000 and Rs 10,000 per 360 days by edition; perpetual from about Rs 11,000 | Distribution and multi-godown firms wanting invoicing, e-invoice and e-way bill together | Dated interface; edition upgrades arrive sooner than expected |
| Marg ERP 9+ | Roughly Rs 8,100 basic, Rs 12,600 silver, Rs 25,200 gold one-time, plus annual support | Pharma and FMCG distribution, where batch, expiry and scheme tracking are the job | Highly vertical — overkill without batch and expiry handling |
| Clear (ClearTax) GST | Subscription, quoted on invoice volume and GSTIN count | Several GSTINs needing bulk reconciliation and e-invoicing at scale | Priced for volume; a single-GSTIN shop overpays |
| NIC GePP-On / GePP offline | Free | Businesses just over the e-invoicing threshold with few invoices | E-invoices only — no books, inventory or returns |
Two rules we hold to. Pick software your accountant can open — a file format your CA cannot read costs more in reconciliation hours than any licence saves. And never buy a compliance suite to solve a bookkeeping problem: if purchase bills are entered three weeks late, no software will make GSTR-2B match.
Free tools on the GST portal that people pay to replace
A surprising amount of what small businesses buy is already free from GSTN and NIC.
- Returns Offline Tool. From the portal’s downloads section, it builds return data in Excel or CSV offline for JSON upload — useful where connectivity is poor or data entry is done by someone without portal credentials.
- GePP-On. NIC’s free browser-based e-invoice tool at gepp.einvoice1.gst.gov.in, which also works on a phone. It generates and cancels IRNs, creates e-way bills alongside them, prints e-invoices with the QR code and keeps customer and HSN masters. For a handful of B2B invoices a month, it is genuinely sufficient.
- Bulk generation tools. Excel utilities on the e-invoice portal that turn a spreadsheet of invoices into a JSON for bulk upload.
- e-Invoice QR Code Verifier. A free app from the e-invoice portal that reads a supplier’s QR code and tells you whether the IRN is genuine. Thirty seconds at the receiving dock beats a credit dispute a year later.
- Search Taxpayer. Free GSTIN lookup on gst.gov.in showing registration status and filing history. Run it on every new supplier before the first payment.
The habits that make the 20th boring
Invoice numbering. One unbroken series per financial year per place of business, reset on 1 April, no gaps, no manual overrides. If you cancel an invoice, cancel it — never reuse the number. Gaps are the first thing an officer looks for, and they make your own reconciliation impossible.
Credit reconciliation against GSTR-2B. GSTR-2B, not your purchase register, is the basis of what you may claim. Reconcile monthly, never annually. Keep a standing list of suppliers who file late and either move your buying, hold part of the payment until the credit appears, or accept the working-capital cost knowingly. Do not let unmatched invoices sit in “pending” — credit has a statutory time limit and pending items quietly age out.
Bank matching. Every entry should tie to a bank line or a documented cash transaction. This is what makes GSTR-9 a one-week exercise rather than a three-week forensic project, and the only reliable way to catch sales invoiced but never banked.
Document retention. Keep invoices, credit and debit notes, e-way bills, delivery challans, bank statements and return acknowledgements, stored digitally by year and month, each acknowledgement alongside the period it covers. Confirm the retention period with your CA — it runs for years past the annual return.
e-invoicing, e-way bills and what late filing costs
E-invoicing applies where aggregate annual turnover exceeded Rs 5 crore in any financial year from 2017-18 onward, in force since 1 August 2023 under Notification 10/2023-Central Tax. It covers B2B and export supplies, not B2C, and banking, insurance, NBFCs, goods transport agencies, passenger transport and multiplexes sit outside it. Larger businesses face a 30-day window to report an invoice after its issue date. Check your position on the e-invoice portal: turnover in one past year brings you in permanently.
E-way bills are required above Rs 50,000 consignment value, though intra-state thresholds vary by state. Validity runs one day per 200 km for regular cargo and one day per 20 km for over-dimensional cargo. Since 1 January 2025 you cannot generate a bill against a document older than 180 days, and extensions are capped at 360 days.
Late GSTR-1 or GSTR-3B attracts Rs 50 a day (Rs 20 for a nil return), capped at Rs 500 for nil returns, Rs 2,000 up to Rs 1.5 crore turnover, Rs 5,000 between Rs 1.5 and Rs 5 crore, and Rs 10,000 above. Interest under Section 50 runs at 18% a year on tax paid late and 24% where credit was claimed in excess.
The fees are rarely the real cost. Sequencing is: you cannot file the current GSTR-1 while an earlier GSTR-3B is outstanding, so one missed month blocks the next, buyers lose their credit, and persistent non-filing can restrict e-way bill generation and stop goods moving.
Questions we are asked most
Do I actually need e-invoicing?
Only if turnover crossed Rs 5 crore in any financial year since 2017-18, and only for B2B and export supplies. Crossing once brings you in permanently — a later drop does not take you back out.
QRMP or monthly?
QRMP saves filing effort but delays visible credit for buyers unless you use the IFF. Selling mostly to businesses, run QRMP with the IFF every month. Selling to consumers, plain QRMP is fine.
My supplier has not filed. Can I still claim the credit?
If it is not in your GSTR-2B, do not claim it. Chase the supplier, hold the tax portion of payment if your contract permits, and claim in the period it appears. Claiming what GSTR-2B does not support is the fastest route to a notice and interest at 24%.
Is free software enough?
For a single-GSTIN business with modest volume, often yes. Zoho Books has a free tier under Rs 25 lakh revenue, Vyapar’s mobile app is free, BUSY has a free Express edition, and NIC’s GePP tools cover e-invoicing at no cost. Pay when you need multiple users, real inventory, bank feeds or multi-GSTIN reconciliation.
I have returns I never filed. What now?
Deal with them now. Returns become unfileable three years after their due date, and the liability does not disappear with the ability to file. That is a chartered accountant’s job, not a software one.
If my software files automatically, do I still need a CA?
Software files what you feed it. It cannot judge whether a supply is exempt or zero-rated, whether a credit is blocked, whether an HSN classification survives scrutiny, or how to answer a notice. Use software for the routine loop and a CA for judgement.
Verify before you act
Rules move. Before relying on any date, rate or threshold above, check the primary sources: the GST portal for returns, ledgers and the Invoice Management System; CBIC-GST for notifications and circulars; the GST Council for decisions and effective dates; the e-invoice portal; and the e-way bill portal. Where a portal and a summary disagree, the portal wins.
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