India’s Goods and Services Tax (GST) framework is set for another significant upgrade in FY 2025–26. With changes spanning return filing, invoicing, compliance technology, and authentication requirements, it is essential for businesses to stay informed and agile.

This guide outlines what corporate leaders, CFOs, compliance officers, and finance teams must know to navigate the evolving GST Compliance India landscape effectively in 2025 and beyond.

Major Regulatory Updates for GST Filing 2025 and Enhanced GST Compliance

🔹 Three-Year Filing Time Bar

• From July 1, 2025, the GST portal will permanently block the filing of any return that is more than 3 years overdue.
• This rule applies to all key return forms: GSTR-1, GSTR-3B, GSTR-4, GSTR-5/5A, GSTR-6, GSTR-7/8, and GSTR-9.
• Returns pending beyond 3 years will become non-fileable forever—no exceptions or extensions.
• Consequences include permanent loss of ITC, inability to regularize compliance, penalties, and potential legal proceedings.
• Businesses must clear old backlogs before July 2025 to avoid irreversible non-compliance.

🔹 GSTR-3B Auto-Draft Enhancement & Non-Editable Fields from July 2025

• From April 2025, GSTR-3B will auto-populate liability and ITC values based on GSTR-1 and GSTR-2B, with limited room for manual correction.
• Starting July 2025, Table-3 of GSTR-3B becomes non-editable, so errors in GSTR-1 or IFF filings will directly impact tax liability.
• Run mock reconciliations for March 2025 filings to detect and resolve mismatches ahead of system lock-in.

🔹 Mandatory MultiFactor Authentication (MFA)

• From April 1, 2025, Multi-Factor Authentication (MFA) is compulsory for all users accessing the GST portal.
• At least two verification modes (password + OTP/biometric) are required.
• Businesses must update registered contact details and train internal teams on MFA protocols to ensure uninterrupted access.

🔹 Compulsory Input Service Distributor (ISD) Registration

• Effective April 1, 2025, ISD registration is mandatory for entities with multiple GSTINs sharing common input services (e.g., audit, software, security).
• Cross-charging is no longer allowed under revised rules; all ITC distribution must occur through the ISD route.

           Businesses must:

• • Apply using Form GST REG-01
  • Issue ISD invoices under Rule 54(1)
  • Distribute ITC monthly based on turnover
  • File GSTR-6 by the 13th of the following month
  • Ensure recipient units claim the ITC via GSTR-3B

Failure to comply could lead to ITC reversal, penalties up to ₹10,000, and increased audit scrutiny.

🔹 e-Way Bill: Tighter Generation & Extension Cut-Offs + Launch of E-Way Bill 2.0

From January 1, 2025, e-Way Bill generation will be restricted to source documents not older than 180 days; enforcement begins in GST returns from April 1, 2025.

Extension of an e-Way Bill will be allowed only up to 360 days from the original issue date.

Businesses should:

• Update systems to auto-validate document dates
• Set internal alerts for renewals
• Integrate validation into logistics and billing SOPs

The new E-Way Bill 2.0 portal, launching July 1, 2025, offers:

• Real-time sync with the existing portal
• Cross-portal tasks like extensions, transporter updates, and consolidated e-Way Bills
• Full operability during portal downtime
• API availability for seamless ERP integration

🔹 E-Invoicing Threshold Reduced

• E-invoicing is mandatory from July 2025 for businesses with turnover of ₹3 crore+ (down from the previous ₹5 crore threshold); further reduction to ₹1 crore is expected in phased rollout.
• B2B invoices must be reported to the Invoice Registration Portal (IRP) within 30 days for businesses with turnover above ₹10 crore.

Prepare by:

• • Identifying affected businesses using FY 2023–24 turnover
  • Updating SOPs
  • Ensuring ERP and GSTIN readiness
  • Training internal teams to avoid penalties

🔹 Revised Input Tax Credit (ITC) Reconciliation Rules

GSTR-2B is now the only valid basis for claiming Input Tax Credit (ITC); provisional ITC claims are no longer allowed.

Businesses should:

• Align reconciliation processes to GSTR-2B
• Use automated tools to match vendor invoices
• Implement vendor compliance checks and risk-scoring

🔹 Quarterly Return Filing (GSTR-1 and GSTR-3B) – QRMP Scheme Tightened

Under the QRMP scheme, late filing of GSTR-1 for two quarters may lead to automatic suspension.

Best practices:

• Enable automated reminders for due dates
• Review historical filing patterns
• Ensure timely monthly PMT-06 tax payments to maintain scheme eligibility
• Use compliance dashboards to track filings and scores

🔹 Amendments to GSTR7 and GSTR8 Formats

• GSTR-7 now mandates invoice-level details, including the deductee’s GSTIN, invoice number, payment amount, and tax deducted.
• GSTR-8 requires comprehensive data on e-commerce transactions, such as purchaser details and transaction reference numbers.

Businesses must revise reporting to ensure:

• Transparency in TDS/TCS
• Accurate input credit claims
• Fewer reconciliation mismatches

🔹 PAN-Based Aadhaar Authentication Mandate

• Effective July 1, 2025, Aadhaar authentication becomes mandatory for all PAN-linked persons associated with GST-registered entities (e.g., authorised signatories, directors).
• No Aadhaar authentication = No access to file returns or perform actions on the GST portal.

Immediate actions:

• Audit Aadhaar-PAN linkage for all personnel
• Use GSTN tools to verify authentication status
• Complete pending e-KYC before the deadline

🔹 GST Waiver Scheme 2025

• Businesses that have cleared GST dues up to March 31, 2025, may apply for waiver of interest and penalties under SPL01 or SPL02 within three months.
• This is a limited window to regularize past defaults without heavy cost implications.
• Review eligibility and complete applications promptly for maximum benefit.

🔹 Sector-Specific Rate Changes

• Used Car Dealers: GST rate on margin-based transactions has increased from 12% to 18%.
• Hotel Sector: GST will be levied on actual transaction value, not declared tariff.

Rooms priced above ₹7,500/day will attract 18% GST with full ITC.

• • Businesses should update billing systems, pricing structures, and customer communication accordingly.

Technology and Security in GST Compliance India

🔹 New GST Compliance Dashboard (Beta) by GSTN

• 📊 A new GST Compliance Dashboard launched in April 2025 offers real-time compliance scores, anomaly detection, and filing trends.
• ✅ Use the dashboard to spot filing gaps and address systemic compliance issues early.

🔹 Integration with Accounting Software

• 🧾 Leading accounting platforms like Tally, Zoho, and QuickBooks are releasing updates by mid-2025 to support GSTR-3B automation.

🔄 Businesses should:

• Update accounting software
• Ensure ERP-GSTN compatibility
• Conduct mock filings in June to resolve issues early

🔹 Biometric Authentication for GST Registration

• 📸 Biometric verification and photo capture are now compulsory for all new GST registrations, with a strict 15-day deadline.
• ⚠️ Incomplete authentication will block ARN generation and delay onboarding.
• Schedule biometric appointments and complete documentation without delay.
• 👨‍💼 Schedule biometric appointments and complete documentation without delay.

Final Takeaway

GST Filing 2025 is not just about ticking boxes—it is about building a culture of proactive GST compliance in India. For businesses, the path ahead lies in being proactive—upgrading systems, re-evaluating processes, and staying ahead of every change.

By partnering with domain experts like BCL India, companies can ensure smooth compliance, avoid penalties, and unlock strategic financial control in a rapidly evolving GST landscape.