GST Return Filing for Multiple Branches Under One PAN: How TaxBuddy Organises Compliance
- CA Pratik Bharda
- Jan 20
- 9 min read
GST compliance for businesses operating multiple branches under one PAN is no longer limited to simple return filing. Each branch registered in a different state is treated as a distinct person under the GST law, requiring separate GSTIN-wise returns and reconciliations. From April 1, 2025, Input Service Distributor registration becomes mandatory for such entities, adding another layer of compliance. Managing outward supplies, ITC distribution, and statutory deadlines across branches can quickly become complex without structured systems. Platforms like TaxBuddy now play a critical role in organising multi-GSTIN data, ensuring accuracy, and preventing penalties through automated compliance workflows.
Table of Contents
Understanding GST Registration for Multiple Branches Under One PAN
Under the GST law, a single PAN can hold multiple GST registrations depending on how and where a business operates. When branches are located in different states, each location must obtain a separate GSTIN, even though the PAN remains the same. These registrations are treated as distinct persons for GST purposes, meaning transactions between branches are taxable and must be reported separately. For branches operating within the same state, a single GSTIN is generally sufficient unless the business opts for separate registrations for distinct business verticals with independent accounting systems.
When Multiple GSTINs Are Mandatory Under GST Law
Multiple GSTINs become mandatory when a business has operations in more than one state or union territory. GST is a destination-based tax, and state-wise registration ensures correct tax allocation and compliance. Separate GSTINs may also be required when distinct business verticals operate independently within the same state and maintain separate books of accounts. In such cases, registration is optional, but once taken, full compliance applies to each GSTIN independently.
GST Return Filing Requirements for Each Branch GSTIN
Each GSTIN under a PAN must file its own set of GST returns. These include GSTR-1 for outward supplies, GSTR-3B for summary tax liability and payment, and GSTR-9 as the annual return, where applicable. Returns must be filed GSTIN-wise, even if accounts are managed centrally. Any delay, mismatch, or omission for one branch impacts only that GSTIN, but repeated non-compliance can attract audits and scrutiny at the PAN level.
Input Service Distributor Rules Effective from April 1, 2025
From April 1, 2025, Input Service Distributor registration becomes mandatory for businesses with multiple GSTINs under one PAN that incur common input services. Expenses such as legal fees, audit costs, software subscriptions, and corporate office expenses must now be distributed through the ISD mechanism. The ISD is required to issue prescribed ISD invoices and file GSTR-6 monthly, ensuring that input tax credit is allocated to recipient branches based on turnover or other prescribed methods.
How ISD Registration Impacts Multi-Branch GST Compliance
ISD registration fundamentally changes how input tax credit flows across branches. Credit can no longer be distributed through internal accounting adjustments. It must follow statutory allocation rules and be reported through GSTR-6. This increases compliance accuracy but also adds reporting responsibility. Incorrect allocation or delayed filing can block ITC for recipient branches, impacting working capital and increasing reconciliation challenges.
Common Compliance Challenges in Multi-Branch GST Filing
Managing multiple GSTINs often leads to data fragmentation, missed deadlines, and reconciliation issues. Common challenges include mismatches between GSTR-1 and GSTR-3B, incorrect ITC claims, delayed branch-level filings, and errors in inter-branch invoicing. With ISD becoming mandatory, businesses also face challenges in tracking common expenses and applying correct allocation formulas consistently across branches.
Penalties and Risks for Incorrect Multi-GSTIN Filings
Each GSTIN carries independent compliance responsibility. Late filing attracts daily late fees and interest on tax dues. Incorrect ITC claims or non-compliance with ISD rules may trigger penalties under Section 122, departmental audits, or even cancellation of registration in severe cases. Repeated defaults across branches increase the risk of PAN-level scrutiny, leading to broader compliance consequences.
How TaxBuddy Simplifies GST Return Filing for Multiple Branches
TaxBuddy streamlines multi-branch GST compliance by bringing all GSTINs under a single structured workflow. Branch-level data is consolidated, validated, and tracked centrally while ensuring GSTIN-wise filings remain compliant. The platform supports automated return preparation, mismatch detection, and ISD compliance, reducing dependency on manual tracking and minimising filing errors across branches.
Technology-Driven Controls for Error-Free GST Compliance
Automation plays a critical role in multi-GSTIN environments. Central dashboards, GSTIN-wise tracking, auto-validation of invoices, and reconciliation tools help identify discrepancies early. By using structured technology controls, businesses can ensure consistent data flow between branches, timely filings, and accurate ITC distribution without manual intervention.
Compliance Checklist for Businesses with Multiple Branches
A strong compliance checklist is essential for businesses operating multiple branches under one PAN, as GST obligations apply independently to each GSTIN. The foundation begins with maintaining GSTIN-wise books of accounts. Every branch must record its outward supplies, inward supplies, tax payments, and input tax credit separately. This ensures clarity during return filing and makes reconciliations and audits significantly smoother.
Tracking return due dates for each GSTIN is equally important. GSTR-1, GSTR-3B, annual returns, and, where applicable, ISD-related returns such as GSTR-6, all follow specific timelines. Missed deadlines for even one branch can lead to late fees, interest, and system-based restrictions on filing subsequent returns. A central compliance calendar helps avoid such lapses.
Regular reconciliation of branch transactions plays a critical role in preventing mismatches. Sales reported in GSTR-1 should align with tax paid in GSTR-3B, and input tax credit claimed should match supplier data reflected in auto-populated statements. Inter-branch transactions must also be reviewed carefully, as these are treated as taxable supplies under GST and are often a common source of errors.
Registering as an Input Service Distributor, where applicable, is now a key compliance step. From April 1, 2025, businesses with multiple GSTINs under one PAN that incur common input services are required to obtain ISD registration. Once registered, input tax credit on shared expenses must be distributed strictly through ISD invoices and reported in GSTR-6 within prescribed timelines.
Filing GSTR-6 on time is crucial to ensure uninterrupted credit flow to branch GSTINs. Any delay or incorrect filing can block ITC for recipient branches, affecting cash flows and operational planning. Consistent monitoring of ISD filings ensures that credit distribution remains accurate and compliant.
Periodic internal reviews add another layer of protection. Reviewing return filings, ITC utilisation, and compliance status at regular intervals helps identify issues before they escalate into notices or audits. These reviews also help businesses stay aligned with regulatory changes and evolving compliance requirements.
Technology-backed compliance monitoring further strengthens the process. Centralised dashboards, automated alerts, and reconciliation tools help track GSTIN-wise compliance in real time. By reducing manual intervention and increasing visibility across branches, businesses can significantly lower the risk of penalties, avoid operational disruptions, and maintain a stable compliance posture under GST.
Key Regulatory Updates Affecting Multi-Branch GST Filers
Recent regulatory updates have significantly reshaped the compliance landscape for businesses operating multiple branches under one PAN. The most impactful change is the mandatory implementation of Input Service Distributor registration from April 1, 2025, for entities holding multiple GSTINs. This move aims to prevent arbitrary or incorrect distribution of input tax credit arising from common services such as legal, audit, consulting, software, and corporate overheads. Credit distribution is now required to follow prescribed formulas and be reported transparently through GSTR-6, leaving little scope for informal internal adjustments.
Alongside ISD enforcement, invoice-level matching has become more rigorous. Auto-population of data from supplier filings, tighter reconciliation between GSTR-1, GSTR-3B, GSTR-2B, and ISD records, and system-driven validations have reduced tolerance for mismatches. Discrepancies in one branch can delay or block credit availability for another, directly affecting cash flows and working capital across the organisation.
Audit and scrutiny mechanisms have also been strengthened. Multi-branch entities are increasingly being evaluated at a consolidated level, even though compliance remains GSTIN-specific. Repeated errors, delayed filings, or incorrect ITC distribution across branches may trigger audits, demand notices, or penalty proceedings under the Goods and Services Tax framework. The regulatory intent is clear: ensure traceability, accountability, and uniform compliance across all registrations linked to a single PAN.
For multi-branch businesses, staying aligned with these updates is no longer just about filing returns on time. It requires continuous monitoring of regulatory changes, accurate data flow between branches, disciplined record-keeping, and system-driven compliance controls. Failure to adapt can disrupt credit flow, invite enforcement action, and increase operational risk, while timely alignment ensures smoother compliance and financial stability across all branches.
Conclusion
GST compliance for multiple branches under one PAN demands disciplined processes, accurate reporting, and timely filings across every GSTIN. With mandatory ISD registration and stricter enforcement, manual compliance models are increasingly risky. Structured platforms help businesses stay compliant while reducing operational burden. For anyone looking for assistance in tax filing, it is highly recommended to download the TaxBuddy mobile app for a simplified, secure, and hassle-free experience.
FAQs
Q1. Does TaxBuddy offer both self-filing and expert-assisted plans for ITR filing, or only expert-assisted options?
TaxBuddy offers both self-filing and expert-assisted options to suit different levels of complexity and comfort. The self-filing option is designed for taxpayers who prefer control, supported by automated data extraction, validations, and guided steps. The expert-assisted plan is suitable for complex cases or those seeking professional oversight, where a tax expert reviews documents, resolves mismatches, and completes filing on behalf of the taxpayer. Both options are built on the same compliance framework to ensure accuracy and statutory alignment.
Q2. Which is the best site to file ITR?
The Income Tax Department’s e-filing portal remains the official platform for filing income tax returns. However, many taxpayers prefer private platforms that offer structured workflows, automated checks, and human support. Platforms like TaxBuddy are commonly chosen for their ability to simplify document handling, reduce errors through system validations, and provide assistance when issues arise during filing or processing.
Q3. Where to file an income tax return?
Income tax returns can be filed directly on the government e-filing portal managed by the Income Tax Department. Alternatively, authorised private platforms can be used to file returns on the same portal through integrated systems. These platforms act as facilitators, helping taxpayers prepare, validate, and submit returns while ensuring compliance with applicable tax laws and procedural requirements.
Q4. Can multiple branches operate under one PAN for GST?
Yes, a business can operate multiple branches under one PAN. However, the GST law requires separate GSTINs for branches located in different states or union territories. Each GSTIN is treated as a distinct person under GST, even though the PAN remains common. This structure ensures state-wise tax reporting and the correct allocation of tax revenue.
Q5. Is ISD registration compulsory for multi-branch businesses?
From April 1, 2025, ISD registration becomes mandatory for businesses having multiple GSTINs under the same PAN that incur common input services. This includes expenses such as audit fees, legal services, software subscriptions, and corporate office costs. The objective is to ensure transparent and rule-based distribution of input tax credit across branches.
Q6. Which return does an ISD need to file?
An Input Service Distributor is required to file GSTR-6 every month. This return captures details of input tax credit received on common services and its distribution to recipient GSTINs. The filing of GSTR-6 ensures that ITC flows correctly and is reflected in the electronic credit ledger of the respective branches.
Q7. Do branches in the same state need separate GSTINs?
Branches operating within the same state can function under a single GSTIN. Separate GSTINs are required only if the business chooses to register distinct business verticals that maintain independent books of accounts. In the absence of such vertical separation, a single GST registration is sufficient for all branches within that state.
Q8. What happens if one branch delays GST return filing?
GST compliance is GSTIN-specific. If one branch delays filing returns, late fees and interest apply only to that GSTIN. However, persistent delays or defaults can increase the risk of audits, notices, and scrutiny, potentially affecting the overall compliance profile of the business at the PAN level.
Q9. Can ITC be shared across branches without ISD?
No. After April 1, 2025, input tax credit arising from common services cannot be shared across branches through internal accounting adjustments. ITC distribution must be routed through the ISD mechanism using prescribed invoices and reported through GSTR-6. Non-compliance may result in the denial of credit to recipient branches.
Q10. Does each GSTIN require separate accounting records?
Yes, the GST law mandates that each GSTIN maintain its own books of accounts and transaction records. This includes invoices, input tax credit registers, tax payments, and return filings. Separate records ensure accurate reporting, easier reconciliation, and smoother handling of audits or departmental inquiries.
Q11. Can GST compliance be managed centrally for all branches?
GST compliance can be managed centrally using integrated systems or software, even though filings are made GSTIN-wise. Centralised management helps standardise processes, monitor deadlines, and reconcile data across branches, while still meeting the legal requirement of separate GSTIN-level filings.
Q12. How does automation help in multi-branch GST compliance?
Automation helps consolidate data from multiple GSTINs, identify mismatches early, validate ITC claims, and track statutory deadlines. It reduces manual errors, improves reconciliation accuracy, and ensures timely filings. For businesses with multiple branches, automation significantly lowers compliance risk while improving operational efficiency.
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