GST Health Check
& Compliance Review
Most GST problems are invisible until the department sends a notice. TaxClue's GST Health Check scans your registration, returns, ITC claims, invoices, e-way bills, and annual reconciliation — identifying every risk, gap, and missed opportunity before they become demands.
What Is a GST Health Check?
A GST Health Check is a structured, CA-led review of your GST compliance position across every dimension — not just returns filing. The GST department uses automated data analytics to cross-match your GSTR-1, GSTR-3B, GSTR-2B, e-way bills, e-invoices, and annual returns against each other and against third-party Income Tax data. Any mismatch triggers a scrutiny notice automatically.
A Health Check runs the same comparison the department runs — but before they do. It tells you exactly where your compliance has gaps, which gaps carry financial risk, and what to fix first. The result is a written report with a Red / Amber / Green (RAG) rating on every check-point and a prioritised action plan.
The Department's BIFA Analytics Runs 24/7
The GST department's BIFA (Business Intelligence & Fraud Analytics) system automatically cross-matches your GSTR-1 vs GSTR-3B output tax, GSTR-2B vs GSTR-3B ITC claims, e-way bill data vs GSTR-1 invoices, e-invoice IRNs vs GSTR-1, and your Income Tax / TDS data vs GST turnover. A health check runs every single one of these comparisons — giving you the exact picture the department has of your business, before they act on it.
What TaxClue Reviews in Every Health Check
GST Registration & Profile
Return Filing Compliance
ITC Claims & Eligibility
Invoice & Output Tax Compliance
E-Way Bill Compliance
Annual Reconciliation
Highest-Risk Findings in GST Health Checks
Based on TaxClue's reviews across hundreds of businesses, these are the issues found most frequently — and the ones carrying the highest financial exposure when discovered by the department.
ITC Claimed Beyond GSTR-2B
Claiming more ITC than available in GSTR-2B triggers automated DRC-01 notices. Interest at 18% p.a. plus penalty applies on the excess claim.
Section 17(5) Blocked Credits Claimed
ITC on motor vehicles, personal use, club memberships, works contract on buildings — commonly claimed in error. Full reversal + 18% interest required.
GSTR-1 vs GSTR-3B Turnover Mismatch
If GSTR-1 sales exceed tax paid in GSTR-3B, the department auto-calculates a demand on the shortfall with interest — no manual intervention needed.
E-Way Bill vs GSTR-1 Gaps
E-way bills generated without corresponding GSTR-1 invoices suggest unrecorded sales — a classic BIFA analytics flag that triggers ASMT-10.
E-Invoice Obligation Not Met
Turnover above ₹5 Crore mandates IRN-stamped e-invoices for all B2B and export invoices. Manual invoices without IRN are non-compliant.
Rule 42/43 Reversal Not Done
Businesses with both taxable and exempt supplies must reverse a proportionate portion of ITC every month. Most skip this calculation entirely.
Export ITC Refund Not Claimed
Exporters under LUT are entitled to refund of accumulated ITC. Many don't claim it — leaving working capital locked in the government credit ledger.
Inverted Duty Refund Not Claimed
Where input GST rate exceeds output rate, excess ITC accumulates. A Section 54(3) refund can release this locked credit — often worth lakhs.
Incorrect HSN / GST Rate Used
Wrong HSN codes or rates mean either overpayment (recoverable) or underpayment (demand liability). Both require correction through amendments.
TaxClue's 6-Step Health Check Process
- 1
Scoping Call — 30 Minutes
A CA gets on a call to understand your business: industry, turnover, supply types (B2B / B2C / exports / exempt), filing history, and any known issues or received notices. This calibrates which pillars carry the most risk for your specific business profile.
- 2
Data Collection — Portal Access or Exports
We collect: GSTR-1 and GSTR-3B filing data (portal access or JSON / Excel exports), GSTR-2B downloads for the review period, e-way bill report, e-invoice report (if applicable), GSTR-9 / 9C if filed, and your purchase register or trial balance for reconciliation. All data is strictly confidential — NDA available on request.
- 3
6-Pillar Analysis — 40+ Check-Points
Our CA runs through all 40+ check-points across the six compliance pillars. Each receives a RAG rating: Green (compliant), Amber (attention needed), or Red (risk / demand exposure). Financial impact is quantified for every Red and Amber item — not just flagged.
- 4
Risk Quantification
For every Red-rated finding, we calculate worst-case financial exposure: tax payable + 18% interest + applicable penalties. This lets you prioritise — a ₹500 late fee issue is very different from a ₹5 lakh ITC demand risk. The report shows both the issue and its financial consequence clearly.
- 5
Written Report Delivery — Within 72 Hours
A structured written report covering: Executive Summary (overall compliance score), findings by pillar (RAG-rated with financial impact), full 40+ check-point list with status, and a prioritised action plan — written to be immediately actionable, not just diagnostic.
- 6
CA Debrief & Action Plan Agreement
A CA walks you through the report, explains every finding in plain language, and agrees on a prioritised remediation plan. For high-risk items, TaxClue begins corrections immediately — filing amendments, reversals, or notice responses — as part of the engagement.
Health Check Deliverables
RAG Compliance Score Report
Every check-point rated Red / Amber / Green with a single-page executive summary showing your overall compliance health at a glance.
Financial Risk Quantification
Worst-case tax demand + interest + penalty calculated for each Red-rated finding — so you know exactly what's at stake before a notice arrives.
Prioritised Action Plan
Every finding linked to a specific remediation action — file this, reverse this, amend this, claim this — with urgency rating and estimated effort.
ITC Reconciliation Workings
Three-way ITC reconciliation (purchase register vs GSTR-2B vs GSTR-3B) showing every match, mismatch, and recoverable credit with supplier-wise analysis.
E-Invoice / E-Way Bill Gap List
Transactions where e-invoice was not generated (if mandatory) or e-way bill was missing — with the department cross-match output as the department would see it.
CA Debrief Session
30–45 minute call with your reviewing CA to walk through findings, clarify every item, agree on the action plan, and answer any compliance questions.
Health Check ≠ Audit — It's Proactive Protection
A departmental GST audit is adversarial — the officer is looking for tax to demand. A TaxClue Health Check is advisory — finding problems before anyone else sees them. Businesses that do annual health checks have significantly lower scrutiny notice rates because their compliance is genuinely clean. The best time to find a problem is before the government finds it for you.
When Should You Get a GST Health Check?
Just received a GST notice — know your full exposure before responding, not just the specific issue raised.
Before GSTR-9 / GSTR-9C filing — clean your data first, then file confidently with no surprises in the reconciliation.
Before a departmental audit — GST officers give 15 days' notice. A health check in that window lets you walk in prepared.
Business acquisition / due diligence — buying a company? GST liabilities of the target entity become yours after acquisition.
Changed your CA or accountant — know exactly what your predecessor did or missed before you file the next return.
Crossed ₹5 Crore turnover — e-invoice and GSTR-9C are now mandatory. A compliance reset is needed for the new obligations.
Filed a large ITC or refund claim — large claims attract scrutiny. Verify your claim is airtight before the officer reviews it.
Annual proactive review — once a year, whether or not anything looks wrong. The cleanest businesses stay clean by checking regularly.
Business expansion — new states, new products, new customers. Every new dimension adds compliance complexity that needs reviewing.
GST Self-Check — How Healthy Is Your Compliance?
Expand each area below and answer honestly. Any 🔴 or 🟡 item is a potential risk that a CA should review.
One or More 🔴 Items? Act Before the Department Does.
A single Red-rated item can represent months of interest accumulation and a future demand notice. The GST department's analytics runs 24/7 — the moment your return data creates a mismatch pattern, you enter the scrutiny queue. TaxClue's Health Check identifies every Red item, quantifies the financial exposure, and gives you the exact remediation path — so you decide what to fix first and how.
Frequently Asked Questions
A departmental GST audit is adversarial — conducted by a GST officer whose mandate is to identify tax shortfalls and raise demands. A TaxClue Health Check is advisory and confidential — conducted on your behalf to find problems before the department does. The findings stay entirely with you — you decide what to correct, disclose, or respond to. A departmental audit requires you to respond under legal obligation. A health check gives you control of the narrative before any obligation arises.
For a standard 12-month health check, we need: GST portal access (view-only is sufficient) or exports of GSTR-1, GSTR-3B, and GSTR-2B for the period, e-way bill and e-invoice data (portal export), and a trial balance or purchase register for ITC reconciliation. We do not need raw invoice data, banking details, or anything beyond GST compliance records. All data is strictly confidential — we sign an NDA on request.
Finding a liability through a health check is far better than the department finding it — because you have options. If discovered voluntarily before a notice, you can amend returns or make voluntary disclosure — in most cases, this significantly reduces or eliminates penalties. Under GST law, voluntary payment before a notice typically attracts nil or minimal penalty compared to post-notice payment which can attract up to 100% penalty. TaxClue explains the exact remediation path for every finding and its penalty implications so you can make an informed decision.
Yes — a health check is even more critical once a notice is received. The notice tells you what the department found on one specific issue. A health check tells you what else they might find when they dig further — because responding to a notice often triggers a wider review. TaxClue focuses the health check on the notice's subject matter and the three to four surrounding compliance areas that departments typically investigate as follow-up, so your response is prepared for the full scope of inquiry — not just the stated notice issue.
For most businesses, once a year — ideally after the financial year ends and before GSTR-9 filing (July–October window). This lets you reconcile the full year's data, clean any issues, and file the annual return with confidence. Businesses with higher risk profiles — turnover above ₹5 Crore, export-import activity, exempt supplies, or prior department notices — benefit from a half-yearly review. TaxClue includes an annual health check in its ongoing compliance retainer packages at no extra cost for retainer clients.
Typically 48–72 hours from data collection to written report delivery for businesses with turnover up to ₹20 Crore. For larger businesses with complex supply chains, multiple GSTINs, or significant export-import activity, allow 5–7 working days. The scoping call can happen the same day you reach out and data collection typically takes 1 working day. The scoping call → data collection → analysis → report → debrief cycle is designed to complete within one working week for most clients.
Your GST Health Check. 72-Hour Report. Written. Actionable.
6 pillars. 40+ check-points. Red / Amber / Green on every issue. Financial exposure quantified. Action plan prioritised. One call to book.
🔒 Fully Confidential · 4.9★ Google Rating · Written Report · CA-Led