GST Compliance Checklist FY 2025-26: 15 Critical Checks Before 31 March 2026


Every year, thousands of Indian businesses receive GST demand notices — not because they evaded tax, but because they missed a small compliance step before 31 March.

FY 2025-26 is no different. Tighter ITC reconciliation norms, mandatory e-invoicing for businesses above ₹5 crore, and increased portal-based scrutiny mean there's very little room for error this year.

Our team at GetMyCA recently helped a Delhi-based pharmaceutical distributor avoid ₹8.2 lakh in ITC disallowance — simply by running a GSTR-2B reconciliation six weeks before year-end. That's the difference a timely review makes.

We've put together this GST compliance checklist for FY 2025-26 based on the exact framework our Chartered Accountants use for year-end reviews. Go through each check before 31 March — and go into the new financial year clean.

Why This GST Year-End Checklist Matters

A GST year-end review helps you catch filing errors, ITC mismatches, and pending compliances before the financial year closes. Correcting mistakes after 31 March attracts 18% interest per annum and penalties up to ₹10,000 per return.

Here's what's at stake in FY 2025-26 specifically:

  • ITC mismatches between GSTR-2B and GSTR-3B now trigger automatic ASMT-10 scrutiny notices
  • E-invoicing violations carry a penalty of ₹10,000 per non-compliant invoice
  • Unanswered SCNs convert into ex-parte demand orders — which are expensive to reverse
  • GSTR-9 (Annual Return) is due by 31 December 2026, but monthly data errors can't be fixed after the year closes

The 15-Point GST Compliance Checklist for FY 2025-26

1. GSTR-1 Filed for All Months (April 2025 – February 2026)

Log into gst.gov.in → Services → Returns Dashboard. Confirm GSTR-1 is filed for every month. Missing even one month blocks your buyer's ITC and attracts ₹50/day late fee.

2. GSTR-2B vs. Purchase Register Reconciliation

This is the single most important check. Download GSTR-2B for all months and match it against your purchase register. Any ITC claimed beyond what appears in GSTR-2B will be disallowed with 18% interest.

3. GSTR-3B Filed With Correct Tax Payment

All GSTR-3B returns from April 2025 to February 2026 must be filed. Cross-check the figures against your GSTR-1 and GSTR-2B — mismatches trigger automatic scrutiny.

4. GST Registration Details Are Up to Date

Verify your legal name, address, HSN/SAC codes, and authorised signatory's DSC validity on the portal. An expired DSC in March is a compliance emergency no one needs.

5. Blocked Credits Under Section 17(5) Reversed

Check whether you've inadvertently claimed ITC on personal vehicles, food & beverages, club memberships, or construction services. These are blocked credits — reverse them before 31 March to avoid interest.

6. E-Invoicing Compliance Verified

If your turnover exceeds ₹5 crore, every B2B invoice must carry a valid IRN and QR code from the Invoice Registration Portal (einvoice1.gst.gov.in). Pull a sample of 10–15 invoices per month and verify. Retroactive IRN generation isn't possible.

7. GSTR-1 Output Tax Matches Books of Accounts

Run a month-by-month comparison of your GSTR-1 filed data against your accounting software. Even a ₹30,000 discrepancy creates problems during GSTR-9 filing.

8. RCM Liability Identified and Paid

If you've paid freight to a GTA, engaged an advocate, or received services from an unregistered vendor — you likely have Reverse Charge Mechanism (RCM) liability. Cross-check your expense ledger and confirm RCM tax has been paid and filed.

9. HSN/SAC Summary Correctly Reported in GSTR-1

4-digit HSN for turnover below ₹5 crore, 6-digit for above. Verify Table 12 of your GSTR-1 is correctly filled for every quarter. Wrong codes cause GSTR-9 reconciliation errors.

10. GSTR-9 and GSTR-9C Data Prepared

GSTR-9 is mandatory for turnover above ₹2 crore. GSTR-9C (CA-certified) is required above ₹5 crore. Both are due 31 December 2026 — but you need clean FY 2025-26 data now to file them accurately later.

11. Export Refund Applications Filed (Zero-Rated Supplies)

RFD-01 refund claims have a strict two-year window. Invoices from April 2023 crossed that deadline in April 2025. Review all pending export refund applications immediately and escalate any approaching the cutoff.

12. APOB and VPOB Registrations Audited

E-commerce sellers storing inventory in Amazon or Flipkart warehouses need GST registration in each warehouse state. Audit your active registrations against your current warehouse states — any gap means undeclared interstate supply.

13. Cash Ledger and Credit Ledger Reconciled

Download your electronic cash and credit ledger statements from gst.gov.in and match them against your books. Excess cash ledger balance can be claimed as a refund through RFD-01.

14. Pending Notices and SCNs Reviewed

Go to Services → User Services → View Notices & Orders on the portal. Check for DRC-01 (demand notice), ASMT-10 (scrutiny), or REG-17 (cancellation notice). Unanswered notices become demand orders — respond before the deadline.

15. March 2026 Return Data Validated Before Month-End

Don't wait until April to prepare March data. Finalise your sales register, calculate ITC from GSTR-2B, and capture any pending reversals or RCM payments in the March GSTR-3B. This is your last opportunity to correct the full year.

Quick Reference Table

#CheckKey DeadlinePenalty If Missed
1GSTR-1 all months filed11th each month₹50/day + buyer ITC blocked
2GSTR-2B reconciliationBefore 31 March 2026ITC disallowance + 18% interest
3GSTR-3B filed correctly20th each month₹50/day + interest
6E-invoicing complianceEvery invoice₹10,000 per invoice
8RCM paid and filedBefore 31 March 2026Hidden demand + interest
14Notices reviewedImmediateEx-parte demand order

Professional Help vs. DIY — Which Makes Sense?

For businesses with turnover above ₹1 crore, multi-state registrations, export transactions, or e-commerce operations — a professional year-end review almost always costs less than the penalty of a missed compliance.

A CA-led review covers all 15 checks, identifies ITC mismatches you'd likely miss, and handles any notices professionally. The typical cost: ₹5,000–₹25,000. The typical cost of getting it wrong: several times more.

Conclusion

Three things to do today:

  • Run your GSTR-2B reconciliation — this one check protects more money than anything else on this list
  • Check your GST portal inbox for pending notices — unanswered SCNs become demand orders fast
  • Prepare your March 2026 return data now — don't leave corrections to the last week of April

With 240+ projects and 150+ clients served across India, GetMyCA has built its reputation on exactly this kind of hands-on compliance support. Our Chartered Accountants — CA Gaurav Gupta (Indirect Tax) and CA Neha (Direct Tax & Due Diligence) — bring the experience your year-end review needs.

For the full checklist with step-by-step guidance on each item, visit our GST compliance checklist FY 2025-26 resource page.

Have questions? Drop them in the comments or reach out at paras@getmyca.com — we respond within 24 hours.

Comments

Post a Comment

Popular posts from this blog

Complete Guide to Refund of ITC on Account of Inverted Duty Structure

Image
Are you struggling with accumulated Input Tax Credit (ITC) due to an inverted duty structure in your business? You're not alone. In my 12 years of experience as a GST consultant, I've helped over 200 manufacturing businesses recover millions in blocked ITC through proper refund mechanisms. This comprehensive guide will walk you through everything you need to know about claiming refunds when facing an inverted tax structure under GST. Understanding Inverted Duty Structure: The Basics An inverted duty structure occurs when the GST rate on inputs (raw materials, components, or services) is higher than the GST rate on the final output products. This creates a situation where businesses accumulate excess Input Tax Credit that cannot be utilized against output tax liability, leading to blocked capital. Real-World Example: When I worked with a pharmaceutical manufacturer in 2024, they were purchasing active pharmaceutical ingredients (APIs) at 12% GST but selling finished medicines ...
Read more

GST Refund on Corrugated Boxes: Complete Guide for Indian Manufacturers (2026)

Image
 India's corrugated box industry is the backbone of packaging for e-commerce, pharma, FMCG, and electronics sectors. But thousands of manufacturers are unknowingly losing lakhs of rupees every year due to a GST mismatch called the Inverted Duty Structure (IDS). Here is the problem: raw materials like kraft paper, duplex board, and adhesives attract 18% GST, while finished corrugated boxes are taxed at only 5% under HSN 48191010. This rate difference causes Input Tax Credit (ITC) to accumulate in your Electronic Credit Ledger every month — silently blocking your working capital. The Eastern India Corrugated Box Manufacturers Association (EICBMA) has warned that this IDS issue has put over 20,000 MSMEs at serious financial risk. What is the Solution? Under Section 54 of the CGST Act, every registered corrugated box manufacturer who is not under the Composition Scheme can legally claim a refund of this accumulated ITC. This is not a benefit — it is your right. With GST 2.0 effect...
Read more

Footwear Industry GST Update 2025: Why Your Business Needs Professional Compliance Support

Image
The phone call came at 8:47 AM on October 15, 2024 a footwear manufacturer in Noida had just received their first notice under the newly implemented GST scrutiny framework. Despite running a compliant operation for seven years, the enhanced automated surveillance system flagged a ₹3.2 lakh discrepancy in their Input Tax Credit reconciliation. This wasn't negligence; it was the inevitable result of navigating 2025's dramatically transformed GST landscape without specialized guidance. The Footwear Industry GST Update 2025 represents the most significant regulatory shift since the tax regime's inception in 2017. With stricter compliance requirements, reduced e-invoicing thresholds, and AI-powered scrutiny systems, footwear businesses face unprecedented challenges that demand professional expertise. This comprehensive analysis explores the critical changes affecting footwear manufacturers, wholesalers, and retailers—and why professional compliance support has evolved from optio...
Read more