How to File GST Returns for Multiple GSTINs?

In India, businesses operating in more than one state or having multiple branches are often required to obtain various GSTINs (Goods and Services Tax Identification Numbers). Each GSTIN corresponds to a unique registration under GST for each state or union territory. All GST Returns, GSTR-1, GSTR-3B, and GSTR-9 must be filed accurately and on time to avoid late fees and cancellation of registration.

In this blog, we will explore the types of GST Returns, their due dates, required documents, and a step-by-step process for filing GST returns for multiple GSTINs.

What is a GSTIN?

GSTIN stands for Goods and Services Tax Identification Number. It is a 15-digit unique identification code provided to every registered business entity under GST. Businesses require a separate GSTIN for each state in which they operate. For example, if a company operates its business in Maharashtra and Delhi, it must obtain a separate GSTIN for each state.

Why Are Multiple GSTINs Required?

A business is required to take a separate GST registration:

• For each state from which taxable supplies are made.
• If it operates distinct business verticals within the same state.
• When the threshold limit for GST registration is exceeded in different states.
• If it operates as a distinct legal entity in various states

Types of GST Returns to be Filed

Each GSTIN must file the applicable returns independently:

• GSTR-1 (Monthly/Quarterly): Outward supplies of goods/services
• GSTR-3B (Monthly): Summary return including sales, purchases, ITC, and tax liability
• GSTR-9 (Annually): Annual return
• GSTR-9C (Annually for turnover > Rs. 5 Cr): Reconciliation statement

GST Return Type & Due Dates

– Annual, TDS/TCS, ISD & others: See chart below:

Form	Frequency	Due Date
GST-1	Monthly or Quarterly	11th day of the succeeding month 13th of the month succeeding the quarter
GST-1A	Monthly or Quarterly	After filing GSTR-1 and until the filing of GSTR-3B
GSTR‑3B	Monthly	Due on the 20th of each month
GSTR‑4	Composition	30th June of the succeeding year
GSTR‑5	Non-resident	20th of the succeeding year
GSTR‑6	ISD	13th of the succeeding year
GSTR‑7	TDS Deductors	10th of the succeeding year
GSTR‑8	E‑commerce	10th of the succeeding year
GSTR‑9 & 9C	Annual & Audit	Dec 31 next FY
GSTR‑10	Cancellation	Within 3 months from the date of cancellation or surrender of GST registration
GSTR‑11	UIN holders	28th of the month succeeding the month in which the UIN holder receives the inward supply.

Documents Required to File GST Return

You will need the following documents to file GST return online:

1. Sales Invoices (B2B, B2C, Exports)
2. Purchase Invoices
3. Credit Notes and Debit Notes
4. Expense Bills (Eligible for ITC)
5. GST Payment Challans (PMT-06)
6. Bank Statements (For verifying tax transactions)
7. e-Invoices and e-Waybills
8. Input Tax Credit Register
9. Stock Register
10. Import/Export Documents (BOE, shipping bills)
11. Branch Transfer Records
12. Reconciliation Reports (GSTR-2A/2B vs. Purchase)
13. Previous Return Filing Copies (for carry forward)
14. HSN/SAC Code Mapping Sheets
15. Digital Signature Certificate (DSC) or EVC-Enabled Mobile Number/Email ID for verification

Step-by-Step Guide to Filing GST Returns for Multiple GSTINs

Managing GST compliance across multiple states can be overwhelming for businesses that hold more than one GST Identification Number (GSTIN). To make this process manageable, here’s a detailed guide to filing GST returns for multiple GST registrations in India.

Step 1: Maintain Separate Books of Accounts for Each GSTIN

The first and most essential step is to segregate your financial records GSTIN-wise.

• Maintain dedicated sales and purchase ledgers, stock registers, tax invoices, credit/debit notes, and expense vouchers for each GSTIN.
• This ensures clarity in reporting and helps with error-free reconciliation during filing.
• Keep a record of inter-branch transfers between GSTINs, if applicable.

Step 2: Collect and Organise Required Documents

Before initiating the return filing, gather the required documents and data for each GSTIN. A consolidated list is provided at the end of this guide.

Step 3: Choose a GST Filing Tool with Multi-GSTIN Support

Filing returns manually for each GSTIN is not just time-consuming, but also increases the risk of clerical errors.

• Use GST compliance software that supports multi-GSTIN management.
• This software is equipped with:
• Central dashboards for tracking the return status for each GSTIN
• Automated validations and mismatch alerts
• PAN-level analytics and reconciliation tools

Step 4: PAN-Level Data Consolidation

Advanced GST software platforms enable the extraction of data from multiple GSTINs associated with the same PAN.

• This helps consolidate input and output tax data.
• PAN-level reports help identify anomalies or mismatches across different branches or units.
• It also enables efficient bulk upload and data mapping, especially useful for businesses filing GSTR-1, GSTR-3B, and GSTR-9 for multiple locations.

 Step 5: Auto-Populate GST Forms GSTIN-Wise

Instead of entering details manually for each GSTIN, use the auto-fill feature:

• Auto-import sales data from your accounting system or e-invoicing portal.
• Populate GSTR-1 (outward supplies) and GSTR-3B (summary return) using structured templates.
• Verify tax liabilities, input tax credit, and net tax payable for each GSTIN before submission.

Step 6: Validate and Reconcile the Data

Each GSTIN will have its tax liabilities and credits, so cross-verification is crucial:

• Match purchase invoices with GSTR-2B auto-generated statements for each GSTIN.
• Reconcile the outward supplies and inward tax credit before finalizing returns.
• Check for missed invoices or errors that could lead to mismatches.

Step 7: File Returns Individually for Each GSTIN

Despite having one PAN, GST returns must be filed separately for each registered GSTIN:

• Log in to the GST portal using each GSTIN and submit the appropriate returns (GSTR-1, GSTR-3B, etc.).
• If you are using software, it will auto-navigate the filing steps GSTIN-wise.
• Pay any net tax liability due for each GSTIN before or during GSTR-3B submission.

 Step 8: Save Acknowledgments and Track Filing Status

Once returns are filed for each GSTIN:

• Save the ARN (Acknowledgement Reference Number) for each submission.
• Track return status on the GST portal or through your filing software.
• Download filed returns

Penalties for Non-Compliance

Failure to file GST returns for each registered GSTIN can lead to significant legal and financial consequences, such as:

1. Late Filing Fees:

• A late fee of ₹50 per day per return (₹25 CGST + ₹25 SGST) is levied for delayed filings.
• For nil returns, the late fee is reduced to ₹20 per day (₹10 CGST + ₹10 SGST).
• The maximum late fee can go up to ₹5,000 per return.

2. Interest on Tax Liability:

• Interest at the rate of 18% per annum is charged on the delayed payment of tax from the due date till the actual date of payment.
• If excess Input Tax Credit (ITC) has been claimed or output tax liability is underreported, interest applies.

3. Suspension of GSTIN:

• Persistent default in return filing can result in the temporary suspension of the GST registration, during which no business operations are allowed.

4. Cancellation of GST Registration:

• Continued non-compliance may lead to cancellation of GST registration, especially if returns remain unfiled for more than six consecutive months (three for composition dealers).
• Once cancelled, the taxpayer has to apply for fresh registration and cannot legally operate under the cancelled GSTIN.

5. Ineligibility for ITC:

• Filing delays may disqualify a business from availing Input Tax Credit (ITC), as vendors may not reflect the relevant transactions in GSTR-1, leading to mismatches in GSTR-2 B.

Conclusion

Although filing GST returns for several GSTINs may appear complicated, it is possible with the correct strategy and procedures in place. Maintaining compliance with the GST laws in each state is crucial, regardless of whether your company operates in many states or throughout India. You can simplify your GST compliance and steer clear of needless legal problems by filing on time, maintaining accurate data, and utilising technology or expert assistance.