Mid-Year GST Audit Checklist 2025: Get FY 2025–26 Ready
- Introduction to the Mid-Year GST Audit Checklist
- Mid-Year GST Deadlines to Watch (July–Sept 2025)
- Reconciliation Steps for April–June 2025 Returns
- Input Tax Credit (ITC) Cleanup Before September
- e-Invoice & e-Way Bill Checks (New Rules 2025)
- Common GST Audit Red Flags to Eliminate Mid-Year
- Final Audit-Ready Checklist for July–August 2025
- FAQ: Mid-Year GST Audit Planning (India)
- Conclusion
Introduction to the Mid-Year GST Audit Checklist
As we enter Q2 of FY 2025–26, July is the optimal time for proactive GST audit readiness. Most businesses wait until December to fix gaps—but that’s often too late. A mid-year review, especially of the April–June GST data, helps prevent compliance issues, safeguards Input Tax Credit (ITC), and prepares for seamless year-end filings.
This mid-year GST audit checklist for 2025 is designed for CA firms, SME finance teams, and internal audit leads who want to stay ahead of audit season and ITC reconciliation stress. Here’s how to get your books in shape now—before deadlines pile up.
Mid-Year GST Deadlines to Watch (July–Sept 2025)
Here are the critical GST dates from July to September:
| Due Date | Return/Form | Key Action |
|---|---|---|
| 11th monthly | GSTR-1 | Upload outward supplies (April–June recheck) |
| 20th monthly | GSTR-3B | Tax payment + ITC declaration |
| September 30 | ITC Deadline | Last chance to claim FY 2024–25 ITC |
| Quarterly IFF | QRMP filers | Final reconciliation for Q1 |
Reconciliation Steps for April–June 2025 Returns
Start by checking whether your returns match internal books:
GSTR-1 vs books of accounts: Ensure outward supplies are correctly uploaded.
GSTR-3B vs GSTR-2B: Compare your claimed ITC vs eligible ITC in the portal.
Tax liability vs payment made: Ensure no shortfall that could attract interest.
Suggested Reconciliation Tracker:
| Reconciliation Area | Status | Action Required |
|---|---|---|
| GSTR-1 vs Sales | ✅/❌ | Revise GSTR-1 if needed |
| 2B vs 3B ITC | ✅/❌ | Reverse excess ITC in 3B |
| Credit Notes matched | ✅/❌ | Upload pending ones |
Input Tax Credit (ITC) Cleanup Before September
Now is your best chance to clean your ITC records before the September 30 cutoff for FY 2024–25 claims.
How to claim or reverse ITC before September:
Ineligible ITC (blocked credits under Rule 42/43) must be reversed.
Unclaimed credits from FY 2024–25 must be verified and claimed this quarter.
180-day ITC rule: Reverse credit where payment hasn’t been made to vendors within 180 days.
- Cross-check with vendor invoices, especially for imports and capital goods.
e-Invoice & e-Way Bill Checks (New Rules 2025)
Compliance with new thresholds and rules introduced in 2025 is crucial:
e-Invoicing now mandatory for businesses with turnover above ₹5 crore
Ensure QR code and IRN are present on all B2B invoices
e-Way bills must match invoice data, especially for exports and interstate trade
Common GST Audit Red Flags to Eliminate Mid-Year
Fixing these issues now can prevent notices later:
GSTR-1 not matching 3B (inconsistent sales figures)
Zero-rated supplies with no LUT or shipping bill evidence
Excess ITC claims without matching 2B
Round-tripping or fake invoice vendors
Non-payment of tax under RCM
Run an internal red-flag report and classify issues by risk level.
Final Audit-Ready Checklist for July–August 2025
Here’s a print-ready version of your mid-year GST audit checklist:
- Reconcile April–June GSTR-1, 3B, and 2B
- Verify all ITC claims and reverse ineligible credit
- Ensure e-invoice compliance for B2B and exports
- Update vendor payment status (180-day ITC rule)
- Document internal audit working papers and registers
- Use tools to automate reconciliation wherever possible
- Review common audit red flags and rectify issues
- Lock corrected data before the September 30 ITC deadline
FAQ: Mid-Year GST Audit Planning (India)
Q1: Is mid-year GST reconciliation mandatory?
No, but it’s highly recommended to prevent year-end audit pressures and ITC disallowance.
Q2: What happens if I miss the September 30 ITC deadline?
You lose the right to claim pending ITC for FY 2024–25, even if eligible.
Q3: Can I revise GSTR-3B for previous months?
No, GSTR-3B is non-revisable. Corrections must be made in the current month’s return.
Q4: Do SMEs need to follow e-invoice rules in 2025?
Yes, if turnover exceeds ₹5 crore as per latest thresholds.
Conclusion
Preparing for a GST audit mid-year isn’t just smart—it’s strategic. With ITC rules tightening and compliance systems evolving fast, July–August is your best window to clean up, reconcile, and lock your GST position for FY 2025–26.
Avoid audit notices. Maximize eligible credit. Set up clean books before Q3 hits.