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Step-by-step guide to GST filing

Monthly GST workflow
Add InvoicesAuto RCM + ITC Alerts2B Recon + Hard-LockCheck Mismatch & ComplianceFile GSTR-1 by 11thFile GSTR-3B by 20thGSTR-9 by Dec 31 (annual)

Step 1.Set up your business profile

Before filing anything, make sure your business details are correct.

  • Your GSTIN, legal name, and return frequency are pre-configured by your CA.
  • If any detail looks wrong, contact support — do not guess.

Step 2.Add your sales invoices (GSTR-1)

Every invoice you raised to a customer this month must be entered here.

  • Go to Invoices → Sales → click "Add Invoice".
  • Fill in: Customer name, GSTIN (if B2B), invoice number, date, taxable value, and tax amounts.
  • For B2B invoices (to registered businesses), customer GSTIN is mandatory.
  • For B2C invoices (to individuals / unregistered), GSTIN can be left blank.
  • Repeat for every sales invoice in the period.

Import via CSV coming soon. For now, add invoices one by one or ask your CA to bulk-import.

Step 3.Add your purchase invoices

Every purchase invoice from a supplier must be entered to claim Input Tax Credit (ITC). BeMyCa auto-classifies RCM and checks ITC expiry on every save.

  • Go to Invoices → Purchases → click "Add Invoice".
  • Fill in: Supplier name, GSTIN (mandatory for ITC), invoice number, date, taxable value, and tax amounts.
  • ITC can only be claimed if your supplier has filed their GSTR-1 (shown in GSTR-2B).
  • RCM is auto-detected: if the HSN/SAC code matches a Section 9(3) category (GTA, legal, arbitral, etc.) the Reverse Charge flag is set automatically — no manual checkbox needed.
  • ITC time-bar is checked on save: invoices within 60 days of the 1-year Section 16(4) deadline get an expiry warning; past the deadline, ITC is auto-blocked.

Run GSTR-2B reconciliation after adding purchases to verify which invoices are confirmed by the government portal.

Step 4.Review auto-classifications & ITC expiry alerts

BeMyCa flags RCM invoices and blocked ITC automatically. Review these before reconciliation to avoid claiming ineligible credit.

  • Go to Compliance → ITC Expiry Alerts to see all invoices expiring soon or already lapsed.
  • Lapsed invoices are automatically blocked from ITC — verify with your CA before the period closes.
  • Expiring Soon invoices (within 60 days) should be matched against GSTR-2B immediately.
  • For RCM invoices: confirm the Reverse Charge checkbox is set; you must pay RCM tax directly even if you later claim it as ITC.
  • Section 17(5) blocked ITC (club memberships, personal use, works contract for immovable property) shows as itc_blocked_reason — these cannot be claimed.

Section 16(4) time-bar: ITC cannot be claimed after the due date of the September return of the year following the financial year of the invoice.

Step 5.Run GSTR-2B Reconciliation & Hard-Lock

Compares your purchase entries against GSTR-2B, then stamps each invoice per Section 16(2)(aa) — the per-invoice 2B hard-lock.

  • Go to Reconciliation → GSTR-2B Reconciliation.
  • Click "Run Reconciliation" to match your invoices against GSTR-2B records.
  • Review results: Matched (safe to claim), Not in supplier filing (chase supplier), Amount mismatch (verify and correct).
  • Click "Apply 2B Hard-Lock" for the period — each invoice is stamped Matched, Missing-in-2B, or Unverified.
  • Once locked, GSTR-3B automatically excludes Missing-in-2B and Unverified invoices from ITC.
  • For a Missing-in-2B invoice you still want to claim: use "Accept with Risk" — ITC is included but the notice risk is yours.
MatchedConfirmed in GSTR-2B. Safe to claim ITC.
Missing in 2BSupplier hasn't filed. ITC excluded until they do.
Accepted with RiskIncluded in ITC — you accepted the notice risk.
UnverifiedNot yet reconciled. Excluded from GSTR-3B ITC.

Only claim ITC on Matched invoices. The hard-lock automatically handles exclusion — you don't need to manually adjust GSTR-3B figures.

Step 6.Check mismatch report & compliance status

Before filing, verify that GSTR-1 and GSTR-3B outward tax figures don't diverge beyond the 1% GSTN ANSR threshold.

  • Go to Returns → Mismatch Report and select the period.
  • If deviation is within 1% of GSTR-1 tax, status shows "Safe to File".
  • If deviation exceeds 1%: fix the discrepancy in your sales invoices before proceeding — GSTR-3B filing will be blocked.
  • Go to Returns → Compliance Status to see the full dependency checklist for the period.
  • All four must pass: GSTR-1 filed ✓, ITC 2B locked ✓, Mismatch within threshold ✓, GSTR-3B ready ✓.

The filing sequencer blocks GSTR-3B if GSTR-1 is not yet filed for the same period. File GSTR-1 by the 11th first.

Step 7.Compute and review GSTR-1

GSTR-1 is your outward sales return — file it by the 11th. GSTR-3B filing is blocked until this is done.

  • Go to Returns → GSTR-1.
  • Click "Compute GSTR-1".
  • Review the breakdown by invoice type (B2B, B2C Large, B2C Small, Exports).
  • If numbers look correct, click File Return. (Currently mock-filed in demo mode.)

GSTR-1 deadline: 11th of every month for monthly filers. GSTR-3B cannot be filed until GSTR-1 is filed.

Step 8.Compute, review, and pay GSTR-3B

GSTR-3B is the summary return where you pay the net GST liability. Due by the 20th. ITC is automatically computed using your 2B hard-lock status.

  • Go to Returns → GSTR-3B.
  • Click "Compute GSTR-3B".
  • Review the three sections: Outward Tax Liability, ITC Available, Net Tax Payable.
  • ITC Available = GST on Matched + Accepted-with-Risk invoices only. Missing-in-2B and Unverified are excluded automatically.
  • Net Tax = Tax Collected on Sales − ITC from Purchases.
  • Pay the net amount on the GST portal before filing.
  • Click "File Return" once payment is done.

GSTR-3B is blocked if GSTR-1 is unfiled or the mismatch threshold is exceeded. Resolve both before filing.

Step 9.Download PDF invoices & export CSV

Generate professional PDF invoices for any sales entry, and export full invoice lists to CSV.

  • Go to Invoices → Sales. Each invoice row has a download icon — click it to get a PDF.
  • PDF includes business name, GSTIN, customer details, HSN code, IGST/CGST/SGST breakdown, and grand total.
  • Click "Export CSV" to download all invoices for the period as a spreadsheet.
  • Same CSV export is available on the Purchases list.

Use PDF invoices for customer copies. Use CSV export to share with your CA or import into Excel.

Step 10.Review your ITC Ledger

The ITC Ledger shows 12 months of ITC availability, utilization, and net cash paid — in one table.

  • Go to ITC Ledger in the sidebar.
  • ITC Available = total GST on Matched + Accepted-with-Risk purchase invoices for the period.
  • ITC Claimed = ITC set off in GSTR-3B.
  • Net Cash Paid = Tax Liability − ITC Claimed.
  • Running Balance = cumulative unclaimed ITC that carries forward.

If Running Balance is high, you may be over-purchasing or under-utilizing ITC. Check with your CA.

Step 11.Compute GSTR-9 Annual Return

GSTR-9 aggregates all 12 months of outward supplies, ITC, and tax paid. All monthly GSTR-3Bs must be filed before GSTR-9 can be computed.

  • Go to Returns → GSTR-9 Annual.
  • Select the financial year (e.g., 2025-26).
  • Click "Compute GSTR-9" — it pulls data from all monthly GSTR-1 and GSTR-3B returns.
  • Review Table 4 (outward by type: B2B, B2C, exports) and month-wise breakdown.
  • Check filing status per month — filed / pending shown for GSTR-1 and GSTR-3B.

Verify GSTR-9 figures against your GST portal data before submitting. Discrepancies between portal and BeMyCa mean some invoices weren't entered.

GSTR-9 is blocked if any monthly GSTR-3B is unfiled. GSTR-9 is due by 31 December following the financial year end. Late fee: ₹200/day, capped at 0.25% of turnover.

Step 12.Calculate late fee & interest before paying

If you've missed a filing deadline, use the built-in calculator before logging into the portal.

  • Go to Tools → Late Fee & Interest in the sidebar.
  • Select return type (GSTR-1 or GSTR-3B), enter the tax period and actual filing date.
  • For GSTR-3B, also enter tax payable to calculate 18% p.a. interest.
  • Check the "Nil return" box if you had no transactions — lower fee (₹20/day vs ₹50/day).
  • Late fee is capped at ₹10,000 total (₹5,000 CGST + ₹5,000 SGST) under current amendments.

Always calculate the exact amount before making payment on the GST portal to avoid under-payment interest.

Frequently asked questions

What is GSTIN?

A 15-character unique identifier for every GST-registered business in India. Format: 2-digit state code + 10-char PAN + 1 entity type + Z + 1 check digit. Example: 27AABCU9603R1ZX

What is ITC (Input Tax Credit)?

The GST you paid on purchases, which you can deduct from the GST you owe on sales. If you collected ₹10,000 GST on sales and paid ₹3,000 GST on purchases, you only pay ₹7,000 to the government.

What is GSTR-2B?

A government-generated statement showing all purchase invoices your suppliers have filed on your behalf. It's released on the 14th of every month and is the basis for ITC claims.

B2B vs B2C — what's the difference?

B2B (Business-to-Business): sale to a GST-registered buyer — GSTIN required. B2C (Business-to-Consumer): sale to an individual or unregistered buyer — no GSTIN needed. B2C Large = inter-state invoice > ₹2.5 lakh, reported separately.

What is IMS?

Invoice Management System — a GST portal feature where suppliers can push invoices directly to your GSTR-2B. You can accept or reject them. Accepted invoices flow into your ITC automatically.

What if I miss the filing deadline?

Late fee: ₹50/day (₹25 CGST + ₹25 SGST) for returns with tax liability. ₹20/day for nil returns. Plus interest at 18% p.a. on unpaid tax.

What is HSN / SAC code?

Harmonised System of Nomenclature (HSN) for goods, Services Accounting Code (SAC) for services. Required on invoices above ₹5 lakh turnover (4-digit code) or ₹1.5 crore (8-digit code). BeMyCa groups your invoices by HSN in GSTR-1 Table 12 automatically.

What is GSTR-9?

The annual return summarising all 12 months of outward supplies, ITC claimed, and tax paid. Due 31 December after the financial year ends. It must match your monthly GSTR-1 and GSTR-3B filings.

What is Reverse Charge Mechanism (RCM)?

Under RCM, the buyer (not the seller) pays the GST directly to the government. BeMyCa auto-detects RCM based on HSN/SAC code and supplier name (Section 9(3) categories: GTA, legal services, arbitral tribunal, director fees, insurance agents, and others). You still need to pay the RCM tax directly and can claim it as ITC in the same period (if eligible).

What does 'ITC lapsed' mean?

Under Section 16(4), ITC on an invoice cannot be claimed after the due date of the GSTR-3B for September of the year following the financial year of that invoice. BeMyCa auto-blocks lapsed ITC and shows an alert 60 days before the deadline. Once lapsed, the credit is permanently lost — it cannot be carried forward.

What is the GSTR-1 vs GSTR-3B mismatch check?

GSTN's ANSR system compares outward tax in your GSTR-1 (invoice-level) against GSTR-3B (summary return). If the deviation exceeds 1%, GSTN may issue a notice. BeMyCa runs this check before allowing GSTR-3B filing and blocks it if the deviation is too high — so you can fix the discrepancy first.

What is the GSTR-2B Hard-Lock?

Per Section 16(2)(aa), ITC can only be claimed on invoices that appear in your GSTR-2B. The hard-lock stamps each purchase invoice as: Matched (confirmed in 2B, safe to claim), Missing-in-2B (excluded from ITC until supplier files), or Accepted-with-Risk (you've chosen to claim despite absence in 2B, accepting notice risk). GSTR-3B automatically uses only locked-eligible ITC.

Why was my GSTR-3B filing blocked?

GSTR-3B can be blocked for three reasons: (1) GSTR-1 for the same period is not yet filed — file it by the 11th first; (2) GSTR-1 vs GSTR-3B outward tax deviation exceeds 1% — fix the invoice discrepancy; (3) GSTR-2B hard-lock hasn't been applied — run reconciliation and apply the lock first. Check Returns → Compliance Status to see which step is failing.

BeMyCa · GST Filing Assistant · bemyca.cloud · 2026