Any business that has a presence in more than one state is required by law to obtain multiple GST registrations in the state where the business intends to export from. However, only one GST registration number is required for a business unit within the same state. One place may be declared as primary place of business and others as secondary place of business. But if a business needs separate records for each location, even within the same state, it has the option to do so. In cases where a business has more than one vertical, each vertical can be registered and assigned a new GSTIN. 

Each GSTIN is essentially a separate entity from a taxation standpoint. Hence, tax filing and compliances increase with multiple GST registrations, and a good GST accounting software is a must to manage the complexity of maintaining and reporting on multiple entities. While there are plenty of reasons to take multiple GST registration, what's important is to stay compliant with the GST regulations. One of the key compliance responsibilities of GST registered businesses is filing their GST returns. In this article, we will go through the GST return filing for businesses which have more than one GSTIN.

How is return filing for multiple GSTIN different from regular return filing?

Let's start with the basics. All GST registered businesses must file monthly/quarterly returns in GSTR-3B form. Form GSTR-3B is a self-assessment summary of output and input credits that determine GST payment. Similarly, GSTR-1, Statement of Exit must be filed monthly or quarterly. Quarterly filing is for companies that have opted for the QRMP regime. GST returns for multiple GSTIN transactions are different than for single GSTIN transactions. Instead of filing a single return, as in the case of companies with one GSTIN, companies with multiple GSTINs must file returns by GSTIN. In other words, he has to file each declaration separately for each GSTIN. Two separate GSTR-3B for each GSTIN and GSTR-1. For example, if a company has 2 GSTINs, it has to file two declarations. If a company has 5 GSTINs, it has to file 5 separate statements and more. The GSTIN number determines how often a taxpayer must file the same type of return.
When a taxpayer has to claim ITC, he has to do it as per GSTIN. For each GSTIN, he has to apply for ITC separately as the returns are also filed separately. This also applies to GST payments, where each GSTIN refers to an integer part. GST returns, ITC declarations, and payments must be made for each GSTIN more than for.
It is a misconception that all these things can be done in PAN concept. Multiple GSTINs can be registered in one PAN. When it comes to filing returns, claiming ITC, and paying GST, GSTIN is used more than PAN.

Return filing for multiple GST registration

As specified earlier, each GSTIN is essentially a separate entity in the eyes of the tax authorities. Thus, GST returns of multiple entities cannot be clubbed and filed together. A separate return must be filed for each GSTIN your business has. The reason for having separate GSTINs is immaterial here. It could be due to multiple branches in the same state or in different states. What is important is that they are separately registered, and hence their returns must be filed separately.