The financial year-end isn’t just about closing your books — it’s also about ensuring your GST compliance is complete, reconciled, and error-free.
Among the most crucial annual GST filings are GSTR-9 and GSTR-9C.
Many businesses mistakenly treat them as similar, but they serve completely different purposes — and mixing them up can lead to penalties, discrepancies, and compliance risks.
At Aplite Advisors, we’ve assisted hundreds of businesses in streamlining their annual GST filings. One of the most common questions we receive is:
“Do we need to file both GSTR-9 and GSTR-9C? What’s the exact difference?”
Here’s a clear, simplified explanation.
What is GSTR-9?
GSTR-9 is the annual GST return that consolidates all your monthly/quarterly GSTR-1 and GSTR-3B filings for the entire financial year.
It helps verify:
- Outward and inward supplies
- ITC claimed and reversed
- Taxes paid
- Adjustments made in subsequent returns
Who Should File GSTR-9?
All regular taxpayers registered under GST, including SEZ units and developers, except:
- Input Service Distributors (ISDs)
- Casual taxable persons
- Non-resident taxable persons
- Composition taxpayers (they file GSTR-9A — currently optional)
Key Components of GSTR-9
- Summary of outward & inward supplies
- ITC availed and reversed
- Tax paid under CGST/SGST/IGST
- Amendments and adjustments
- Late fees and interest (if any)
Due Date
31st December following the end of the financial year
Example: FY 2024–25 → Due by 31st December 2025
Late Fee / Penalty
| FY Turnover | Late Fee per Day | Maximum Late Fee Cap |
| Up to ₹5 crore | ₹50/day (₹25 CGST + ₹25 SGST) | 0.04% of turnover |
| > ₹5 crore – ₹20 crore | ₹100/day | 0.04% of turnover |
| Above ₹20 crore | ₹200/day | 0.50% of turnover |
What is GSTR-9C?
GSTR-9C is a reconciliation statement, similar to a GST audit.
It compares:
- Figures in GSTR-9
- Figures in audited financial statements
Its purpose is to ensure that your GST returns accurately reflect your books of accounts.
Who Should File GSTR-9C?
Businesses with aggregate turnover above ₹5 crore in a financial year.
Key Components
- Reconciliation of turnover
- Reconciliation of tax paid
- Reconciliation of ITC
- Explanation of differences
- Adjustment entries (if required)
Certification
Part B of GSTR-9C must be certified by a practicing Chartered Accountant or Cost Accountant.
Due Date
Same as GSTR-9 → 31st December
GSTR-9 vs GSTR-9C — A Quick Comparison
| Particulars | GSTR-9 | GSTR-9C |
| Purpose | Annual summary of GST filings | Reconciliation between GSTR-9 and audited books |
| Type | Annual return | Audit & certification statement |
| Who Files? | Regular taxpayers (above ₹2 crore from FY 2024-25 onwards) | Taxpayers with turnover > ₹5 crore |
| Certification Required | No | Yes (CA/CMA) |
| Prepared On | Basis of GSTR-1, GSTR-3B & books | Basis of GSTR-9 & audited financials |
| Due Date | 31st December | 31st December |
| Penalty for Non-Filing | Late fee as per slab | Same slab applies |
| Objective | Reporting compliance | Accuracy & reconciliation compliance |
Why Both Filings Matter
Filing both GSTR-9 and GSTR-9C ensures:
✅ Accurate disclosure of tax liability and ITC
✅ Transparency between books and GST returns
✅ Reduced risk of audits or notices
✅ Stronger compliance credibility during loans, funding, or M&A
✅ Early identification of errors, omissions, or mismatches
Many businesses assume GSTR-9 alone is enough — but GSTR-9C often reveals hidden discrepancies, preventing future litigation.
Common Mistakes Businesses Make
- Turnover mismatch between books and GSTR-9
- Not reconciling ITC with GSTR-2A/2B
- Missing credit notes, advances, or amendments
- Late filing leading to avoidable penalties
- Delay in obtaining CA/CMA certification
Step-by-Step Compliance Checklist
For GSTR-9
✔ Verify GSTR-1 and GSTR-3B data
✔ Reconcile annual turnover
✔ Review ITC availed, reversed, and ineligible
✔ Include amendments and adjustments
✔ File before due date
For GSTR-9C
✔ Reconcile turnover from books vs. returns
✔ Verify ITC adjustments & reversals
✔ Provide explanations for differences
✔ Obtain CA/CMA certification
✔ Upload and file along with GSTR-9
How Aplite Advisors Simplifies GST Annual Compliance
At Aplite Advisors, GST compliance is not just filing — it’s ensuring precision, transparency, and audit readiness.
Our specialised GST team provides:
✅ Complete preparation of GSTR-9 & GSTR-9C
✅ Detailed reconciliation with financial statements
✅ Professional certification & documentation
✅ Review for potential risks or inconsistencies
✅ Accurate, timely, and error-free filing
We ensure your business stays compliant and avoids penalties — with peace of mind throughout the year.
Case Study
Client: Manufacturing Firm | Turnover: ₹8.5 crore
Issue: Missed reconciliation deadlines & ITC mismatches
Our team performed a full GSTR-9C audit and identified:
🔹 ITC discrepancies worth ₹4.2 lakh
🔹 Turnover mismatches due to unrecorded adjustments
Outcome:
✔ No penalties or interest
✔ Successful submission before deadline
✔ No scrutiny or notice issued
✔ Clean compliance record
Talk to Us
Whether you’re a startup or a growing enterprise, your annual GST return is a reflection of your business accuracy.
Let us help you make it accurate, compliant, and audit-ready.
📞 +91-9015036021
🌐 www.apliteadvisors.com
📧 info@apliteadvisors.com
FAQs
Q1. Do all taxpayers need to file GSTR-9C?
No. Only taxpayers with turnover above ₹5 crore must file GSTR-9C.
Q2. Can GSTR-9C be filed without GSTR-9?
No. GSTR-9 must be filed first because GSTR-9C reconciles its figures.
A practicing Chartered Accountant or Cost Accountant.
Q4. What if there’s a mismatch in reconciliation?
The differences must be reported in GSTR-9C, and any additional liability must be paid before filing.
Q5. Is GSTR-9 mandatory even for NIL taxpayers?
Yes, except for categories specifically exempted by GST law.
