As 2025 closes, the compliance landscape under GST has shifted significantly from return-filing reforms to stricter invoice controls, e-way bill timelines, and systemic ITC safeguards. For finance teams, the difference between a clean audit and a penalty rests on proactive checks, timely filings and updated processes. Below is a detailed checklist with context, deadlines and action items to help you close the year with confidence.
| Focus Area | What Changed / Reminder | Action Required (Before 31 Dec 2025) | |
|
Rate Master Update Identifying Undisclosed liability of 24-25 |
GST Council’s rate rationalisation in 2025 (effective 22 Sep 2025) many goods/services shifted tax slabs. Compensation Cess removed. For any updates/ changes or undisclosed liability, then must show in GSTR 9 & make payment via Form DRC-03. |
Review all SKUs / services → update ERP / POS tax master. Communicate to pricing / sales teams. Ensure invoices from Oct–Dec reflect correct rates. If not done timely then the buyer will not be able to claim ITC. Need to cross verify GSTR 1 & 3B with sales ledger and GL. |
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| GSTR-3B / GSTR-1 Reconciliation & Lock on Edits | From July 2025, auto-populated liability/credit in GSTR-3B is non-editable. Corrections only through GSTR-1A / amendment mechanism. | Implement weekly or monthly automated reconciliation between internal sales/purchase ledgers, e-invoice ledger, GST portal data (GSTR-1 / IFF / GSTR-2B/ IMS). Finalise corrections before filing GSTR-3B. | |
| Three-Year Time-Bar for Filing Returns | From July 2025, returns older than 3 years from due date are barred. | Identify any pending returns (GSTR-1, 3B, others) from > 3 years back; file or rectify immediately, else loss becomes permanent. Archive complete documentation for audit. | |
| Invoice Management System (IMS) Readiness | From October 2025, IMS requires explicit Accept/Reject/Pend action on supplier invoices/credits – ITC will depend on accepted invoices. Suppliers and buyers need to coordinate. | Set up internal SOP: Invoice receipt → IMS match → accept/reject logic → record decisions (with remarks). Assign KPIs/owner for IMS match & exception tracking. | |
| Annual Return (GSTR-9 / GSTR-9C) – Reconciliation & Filing | With 2025 notifications and GSTN updates, annual return depends on accurate GSTR-1 / 3B / IMS data; late fees auto-calculate. | Begin reconciliation for FY 2024–25 now: sales, purchases, ITC, e-invoices, IMS statuses. Collate all data for GSTR-9 / 9C. Aim to file well before 31 Dec 2025 to avoid late fees. | |
| E-Way Bill & Logistics / Goods Movement Compliance | From 1 Jan 2025: e-way bills generation restricted to invoices dated within 180 days; extension capped at 360 days. New E-Way Bill 2.0 portal launched 1 Jul 2025. | Review all active e-way bills: ensure none exceed 360-day extension limit. Enforce vehicle / transporter detail updates promptly within portal time limits. Update logistics SOP to track EWB validity and avoid penalties. | |
| E-Invoicing Compliance: Thresholds, Timelines & ERP Integration | As regulations evolve, more taxpayers fall under e-invoicing; delays or wrong format can break ITC chain. | Validate ERP / billing software compatibility with latest IRP schema. Ensure all B2B invoices issued till Dec are reported timely. Perform test e-invoicing, especially for high turnover or new clients. | |
| Input Tax Credit (ITC) Safeguard & Documentation Readiness | With IMS and auto-locking features, ITC eligibility depends on correct invoices and accepted supplier data. | Maintain a detailed purchase register cross-linked with GST portal data (GSTR-2B, IMS status). Archive supplier confirmations, e-invoices, EWB (if goods moved) and proof of payment. Prepare ITC audit-ready documentation. | |
| System & Software Audit: ERP / GST-Portal Integration & Security | Many accounting platforms updated or released 2025 modules to ensure automated compliance and portal compatibility. | Schedule a full system audit test all integrations (sales, purchase, invoicing, returns, GST portal). Ensure authentication, MFA (if mandated), and backups. Run mock filing for Jan 2026 return to check readiness. | |
| Team Training & SOPs: Internal Alignment before Year-End | Complexity increased: IMS, locked returns, e-way bill time constraints, e-invoice obligations. | Conduct internal training / workshop for accounting, sales, procurement, logistics teams. Circulate updated SOPs (invoice → IMS → acceptance; e-way bill generation; vendor onboarding compliance). Allocate ownership & deadlines for each task before 15 Dec 2025. |
Why This Checklist Matters (Overall Impact)
- Avoid Penalties & Late Fees: With locked returns, time-bars and automatic late-fee computation, delays or errors can lead to unavoidable financial impact.
- Secure ITC and Prevent Credit Rejections: IMS-based invoice acceptance and e-way bill/e-invoice compliance ensure that input credits don’t get blocked during audit.
- Ensure Smooth Operations & Supply-Chain Flow: Logistics, procurement and billing teams working with updated SOPs prevents shipment delays, compliance breaches or tax disputes.
- Facilitate Audit-Ready Documentation: A clean, system-driven record trail (invoices, e-way bills, portal screenshots, IMS logs) helps during internal or external audits and reduces risk.
- Build Compliance Discipline & Governance: End-of-year discipline ensures monthly/quarterly routines remain strong, reducing rush-filing, errors and last-minute compliance stress in future years.
By proactively following this year-end GST compliance checklist, finance teams can close 2025 with confidence, ensuring accurate returns, secured ITC, and smooth operations. Staying organized, updating systems, and maintaining proper documentation not only prevents penalties but also strengthens internal controls, setting a solid foundation for seamless compliance in 2026.
Do you know about IRIS GST software solution
It’s a GST Software trusted by top Indian companies! A cloud-based GST software that helps you to automate your GST Return filing, optimise Reconciliation results and increase ITC claim without any hassle. It’s a powerful GST Return filing that supports multiple GST Return filing, PAN level data view, bulk operations, advanced 2A-Purchase Register reconciliation tool, vendor management and gets you 100 % ITC Claims.
How does IRIS GST Software help with GSTR 9?
- One-click download of GSTR 1, 2A, 2B and 3B data
- IMS
- Reports on Tables 6, 10, 11, 13, 17 and 18 helps in auto-population
- In-built audit trail at an invoice level for each entry (Invoice-wise, month-wise and section-wise bifurcation of all values)
- One-click GSTR-9 data upload for all GSTINs
- Need not wait for year-end, you can get all reports at the end of any month
- A checklist of periods for which you have fetched data from GSTN. This is available return-wise for GSTR 1, 2A and 3B
- Comparison between IRIS auto-calculated data and GSTN auto-calculated data
- Quick reports on differences between table 8 of GSTR 9 vs GSTR 2a vs GSTR 2B vs Purchase Register
IRIS GST Software’s GST Reconciliation module has been built considering the requirements of various industries such as manufacturing, pharmaceuticals, automobiles etc., and has market-tested logic to reconcile the buyer-supplier data across various parameters to reduce manual intervention.
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