GST & Indirect Tax · Annual Return & Reconciliation

GST Annual Return & Reconciliation — GSTR-9, GSTR-9C and audit support

Your year of monthly returns has to add up to your books. We prepare the annual GSTR-9 and the self-certified GSTR-9C reconciliation, close the gaps before the department finds them, and stand with you through any departmental audit.

By CA Vijay R Singh, FCA

ICAI Membership No. 153926 | FRN 136869W | Practising since 2013

Quick summary. GSTR-9 is the annual return that consolidates your year’s GST, mandatory once aggregate turnover crosses ₹2 crore. GSTR-9C is a reconciliation between your audited financials and your annual return, mandatory above ₹5 crore. Since FY 2020–21, GSTR-9C is self-certified by the taxpayer, the statutory CA audit was removed, so our role is to prepare and reconcile it accurately, not to certify it. Both are due by 31 December of the following financial year. We also support you through departmental audit (Sec 65) and special audit (Sec 66) if one is initiated.

Is this for you?

📊

Turnover over ₹2 crore

GSTR-9 annual return is mandatory, and worth doing properly even when it is optional below that.

🧾

Turnover over ₹5 crore

GSTR-9C reconciliation is mandatory, tying your annual return back to your audited accounts.

🔎

Books don’t tie to returns

Your GSTR-3B totals and your financials don’t match, and you need the differences explained.

⚠️

ITC mismatch worry

You suspect input credit was over- or under-claimed across the year and want it reconciled before filing.

📝

Audit notice received

A Sec 65 departmental audit (ADT-01) or Sec 66 special audit has been initiated and you need representation.

🏢

Prior year left open

An earlier annual return was missed or filed loosely and you want it cleaned up before scrutiny.

What we actually do

Step	What happens
Data assembly	Pull the full year’s GSTR-1, GSTR-3B and GSTR-2B alongside your books / audited financials.
Three-way reconciliation	Books vs GSTR-1 vs GSTR-3B vs GSTR-2B, outward supplies, tax paid and input tax credit, line by line.
Resolve the gaps	Identify short payments, excess ITC, RCM left out, and credit notes missed, and how each is corrected.
Prepare GSTR-9	Annual return drafted from reconciled figures, with you reviewing before filing.
Prepare GSTR-9C	Self-certified reconciliation statement compiled, differences explained in the prescribed format.
File & archive	Filed by the 31 December due date, with a clean working-paper file kept in case of later scrutiny.

If a difference points to tax actually short-paid, it can be settled voluntarily through DRC-03, far cheaper than letting it surface in a notice. Where a notice has already arrived, that moves into GST notices, DRC-01 & appeals.

GSTR-9 vs GSTR-9C, who files what

Form	What it is	Applies when	Due date
GSTR-9	Annual return consolidating the year’s GST	Mandatory above ₹2 crore aggregate turnover (optional below)	31 December (next FY)
GSTR-9C	Self-certified reconciliation: audited accounts vs GSTR-9	Mandatory above ₹5 crore aggregate turnover	31 December (next FY)
GSTR-9A	Annual return for composition dealers	Composition taxpayers (where notified)	31 December (next FY)

What you get

Full-year three-way reconciliation
GSTR-9 annual return prepared & filed
GSTR-9C reconciliation statement
ITC review, over/under-claim identified
RCM & credit-note check
DRC-03 voluntary-payment working, if needed
Departmental / special audit support
A reconciliation working-paper file

Transparent pricing

Government cost (statutory position)

Filing GSTR-9 / GSTR-9C: no government fee, filing on the GST portal is free
Late fee, if GSTR-9 is filed late: ₹200 per day (₹100 CGST + ₹100 SGST), capped by a percentage of turnover, which timely filing avoids
Any tax short-paid is payable with interest at 18% p.a.; settling it via DRC-03 before a notice avoids penalty

Quoted per engagement

Professional fees depend on your turnover, transaction volume, the number of GSTINs and how clean the year’s data is. You receive a clear written quote after a short scoping call, no hidden charges, no published menu.

Schedule a 15-minute call

Why CA-led

The reconciliation is the whole job, and reconciling GST to audited financials is core Chartered Accountancy work, not data entry
Differences explained, not just filed, we tell you why your books and returns diverge and what it means for tax
Fix it before the department does, voluntary DRC-03 settlement is far cheaper than a post-audit demand with penalty
One firm if an audit comes, the team that reconciled your year is the team that represents you in a Sec 65 / 66 audit

Frequently asked questions

Is GST audit by a Chartered Accountant still required?

No. The mandatory GST audit and CA certification under Section 35(5) of the CGST Act 2017 was removed by the Finance Act 2021, with effect from FY 2020–21. In its place, taxpayers above ₹5 crore turnover file a self-certified reconciliation statement (GSTR-9C). A CA no longer certifies it, but preparing and reconciling it accurately is still skilled work, which is what we do.

Who has to file GSTR-9 and GSTR-9C?

GSTR-9 (annual return) is mandatory for regular taxpayers with aggregate turnover above ₹2 crore, and optional below that. GSTR-9C (reconciliation statement) is mandatory for those above ₹5 crore. Both are filed for each financial year.

What is the due date for the GST annual return?

31 December of the financial year following the one being reported, for example, FY 2025–26 returns are due by 31 December 2026, unless the date is extended by notification.

What does GSTR-9C actually reconcile?

It reconciles the turnover and tax in your audited financial statements against the figures in your annual return (GSTR-9), and reconciles the input tax credit claimed with what your books show. Every difference has to be reported and explained in the prescribed format.

We found tax was short-paid for the year, what now?

You can pay it voluntarily through Form DRC-03 with interest, before the department raises a demand. Doing so generally avoids penalty and closes the exposure. We compute the amount, prepare the DRC-03, and document the reason so the position is defensible later.

What is the penalty for filing the annual return late?

A late fee of ₹200 per day (₹100 CGST + ₹100 SGST), subject to a cap linked to turnover. Any tax found short-paid also carries interest at 18% per annum. Filing on time, with the reconciliation done, avoids both.

What is a departmental GST audit under Section 65?

The department can audit a registered person’s records for a financial year by issuing Form ADT-01. They examine your returns, books and reconciliations and issue findings in ADT-02. We prepare the records, represent you during the audit, and respond to the findings, ideally on the back of a reconciliation we have already done.

Can you fix a previous year that was filed loosely?

Yes, we reconcile the earlier year, quantify any short payment or excess credit, and where tax is due settle it through DRC-03 before it becomes a notice. Cleaning up an open prior year is far easier than defending it under audit.

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Vijay R Singh & Co., Chartered Accountants · FRN 136869W · ICAI M.No. 153926 · Andheri East, Mumbai, in practice since 2013. References are to the CGST Act 2017, IGST Act 2017 and MGST Act 2017, including the Finance Act 2021 amendment to Section 35(5). General information, not tax advice until engaged.