GST Return Filing for E-commerce Sellers

Goods and Services Tax (GST) for e-commerce is a unified tax system that applies to all online sellers operating in India. Whether you sell products or services on platforms like Amazon, Flipkart, Meesho, or your website, GST registration is mandatory. E-commerce sellers are required to:

• Comply with Tax Collection at Source (TCS),
• file regular GST returns, and
• Maintain proper records of sales, returns, and inventory.

Under the GST regime, e-commerce businesses must file monthly or quarterly returns (GSTR-1, GSTR-3B) and reconcile them with TCS statements provided by marketplaces. Accurate and timely filing not only ensures legal compliance but also helps maintain seller credibility, avoid penalties, and qualify for input tax credit benefits.

Why E-commerce GST Filing is Different: Key Rules for Online Sellers

Normal GST rules often differ for online sellers primarily because e-commerce platforms act as facilitators between sellers and buyers, introducing a unique layer of transaction. While traditional businesses may be exempt from GST registration below a certain turnover, this exemption generally does not apply to online sellers.

The annual turnover threshold for GST registration in India is:

• Rs. 40 lakhs for goods (in most states),
• Rs. 20 lakhs for services, and
• Rs. 10 lakhs for special category states (like those in the Northeast).

This rule exists to ensure that every transaction conducted through an e-commerce platform is accounted for within the tax system, promoting transparency and formalising the sector.

Here are the key rules that specifically apply to online sellers:

• Mandatory GST Registration: If you sell goods through an Electronic Commerce Operator, GST registration is compulsory for you, regardless of your annual turnover.
• Tax Collected at Source (TCS): E-commerce operators are required to deduct 1% TCS (0.5% CGST + 0.5% SGST or 1% IGST) on the net value of their taxable supplies made through their platform. You can claim this TCS as a credit when filing your GST returns.
• No Composition Scheme Eligibility for Goods: Generally, if you sell goods through an e-commerce platform, you are not eligible for the GST Composition Scheme, which offers simpler compliance and lower tax rates.

The only exception is for certain specified services where the e-commerce operator is liable to pay tax under Section 9(5) of the CGST Act. For goods, however, it’s compulsory to get GST registered before you start selling on these platforms.

The core difference lies in the mandatory registration and TCS provisions.

Can I Sell on Amazon or Flipkart without a GST Number?

No. If you are selling physical goods on platforms like Amazon or Flipkart, you cannot sell without a GSTIN. These platforms require you to provide a valid GSTIN during seller registration. This rule applies even if your turnover is below the standard GST registration threshold for offline businesses. This is a common question, and the answer is clear: for goods, e-commerce sellers should file GST.

As an e-commerce seller, you primarily deal with these key GST returns:

1. GSTR-1: Declaring Your Sales and Outward Supplies

• This is a monthly or quarterly statement detailing all your outward supplies (sales).
• You must report all your Business-to-Business (B2B) sales with invoice-wise details and consolidate your Business-to-Consumer (B2C) sales.
• It’s crucial for properly reflecting your sales and for the buyer to claim Input Tax Credit (ITC).

2. GSTR-3B: Summarising Your Monthly Tax and Claiming ITC

• This is a summary self-declaration return filed monthly or quarterly, where you declare your total outward supplies, inward supplies subject to reverse charge, and, importantly, claim your ITC.
• This is the form where you reconcile your tax liabilities and pay your GST dues.

3. GSTR-9 and GSTR-9C: Annual Returns

• GSTR-9 is an annual return that consolidates all your monthly/quarterly GSTR-1 and GSTR-3B filings for the entire financial year. It provides a comprehensive summary of your yearly transactions. Filing GSTR-9 is optional for businesses with an annual turnover up to ₹2 crore, but mandatory for those exceeding that threshold.
• GSTR-9C is a reconciliation statement that needs to be filed by taxpayers whose annual turnover exceeds Rs. 5 crore. It reconciles the data in your GSTR-9 with your audited annual financial statements, and is self-certified.

Note: The thresholds for filing GSTR-9 and GSTR-9C are subject to change each year through notifications issued by the CBIC. It’s important to always refer to the latest GST circulars or official updates to confirm the applicable limits for the relevant financial year.

4. Monthly vs. Quarterly Returns

Understanding the difference between the returns:

Filing GSTR-1 accurately is the foundation for correct GST return filing for e-commerce.

The following tables mentioned below are key sections in the GSTR-1 filing for e-commerce sellers, each capturing specific details related to your sales, supplies, and any necessary amendments.

Step 1: Log in to the GST Portal and Navigate to GSTR-1

Start by accessing your GST dashboard to initiate the return filing process.

• Access the GST Portal: Open your web browser and go to the official GST portal (gst.gov.in/)
• Login: Enter your valid username and password to log in.
• Navigate to Returns Dashboard: Once logged in, click on “Services” > “Returns” > “Returns Dashboard.”
• Select Financial Year and Period: On the Returns Dashboard, choose the “Financial Year” and the “Return Filing Period” (month or quarter) for which you want to file GSTR-1.
• Initiate GSTR-1 Filing: Click “PREPARE ONLINE” under the GSTR-1 tile.

Step 2: Report Your Sales Details

Enter all relevant invoice and transaction data with precision to avoid discrepancies.

• Report Your B2B (Business-to-Business) Invoices (Table 4A, 4B, 4C):

• • If you’ve made sales to other GST-registered businesses, you must provide invoice-wise details.
  • Click on the “B2B Invoices” tile.
  • Click “Add Invoice” and enter the buyer’s GSTIN/UIN, invoice number, date, value, place of supply, and applicable GST rate (IGST for inter-state, CGST/SGST for intra-state).
  • Ensure to tick the “Is E-commerce Operator” checkbox and enter the operator’s GSTIN if the supply was made through them.
  • Save each invoice detail.

• Report Your B2C (Business-to-Consumer) Large Sales (Table 5A, 5B):

• • Yes, the Rs. 1 lakh threshold for invoice-wise reporting of interstate B2C sales applies to all goods and services, not just to pan masala, tobacco, or other specified items.

Important Update: As per the 53rd GST Council meeting, this limit was reduced from Rs. 2.5 lakh to Rs. 1 lakh.

Now, if you make an interstate sale to an unregistered customer exceeding Rs. 1 lakh, you must report it invoice-wise in Table 5A/5B of GSTR-1. This change is applicable across the board, not limited to specific product categories.

• Click on the “B2C Large Invoices” tile, click “Add Invoice,” and provide the invoice details, place of supply (state of the customer), and applicable tax rates.

• Report Your B2C (Business-to-Consumer) Other Sales (Table 7A, 7B):

• • This is typically where most of your e-commerce sales to end consumers (unregistered persons) are reported.
  • Click on the “B2C Others” tile.
  • You’ll generally report these sales in a consolidated manner, classified by place of supply (state of the customer) and GST rate.
  • You must also provide the GSTIN of the e-commerce operator for sales made through them.

• Report Credit/Debit Notes (Table 9B):

• • If you issued any credit notes (for returns, discounts, etc.) or debit notes (for upward adjustments) against previously issued invoices, enter their details here.
  • Specify whether they relate to registered or unregistered persons and link them to the original invoice.

• Enter HSN-wise Summary of Outward Supplies (Table 12):

• • You must summarise your goods/services based on their Harmonised System of Nomenclature (HSN) codes. This includes the HSN, description, UQC (Unit Quantity Code), total quantity, total value, taxable value, and applicable tax amounts.

• Report Supplies through E-commerce Operators (Table 14A, 14B – Important for E-commerce):

• • This specific table is crucial for e-commerce sellers. Here, you declare your supplies made through e-commerce operators where TCS is applicable (Section 52).
  • You’ll provide the operator’s GSTIN, net value of supplies, and the tax type (CGST/SGST/IGST). This helps in reconciling with the operator’s GSTR-8.

• Address Amendments (if applicable) (Table 9A, 9C, 10A, 10B, 11A, 11B):

• • If you need to make corrections to invoices or details reported in previous tax periods’ GSTR-1, you will use the relevant amendment tables. This is where you rectify any mistakes from prior filings.

Step 3: Review, Submit, and File Your GSTR-1 Return

Ensure the accuracy of all entered data before final submission to avoid mismatches and notices.

• Generate GSTR-1 Summary: After entering all details, click “GENERATE GSTR-1 SUMMARY.” This creates a summary of all the information you’ve entered.
• Preview GSTR-1: Carefully review the generated summary and the draft GSTR-1 (PDF format). Check for any errors or omissions in your sales data, tax amounts, and HSN summary.
• Acknowledge and Submit: Once you are satisfied that all details are correct, click the “SUBMIT” button. This locks the data and prevents further changes for that period.
• File GSTR-1: After submission, proceed to “FILE GSTR-1.” You will need to file using either:

• • EVC (Electronic Verification Code): An OTP will be sent to your registered mobile number and email ID. Enter the OTP to verify and file.
  • DSC (Digital Signature Certificate): If mandatory or preferred, use your Digital Signature Certificate to sign and file the return.

• Download Acknowledgement: Upon successful filing, an Acknowledgement Reference Number (ARN) will be generated. Download the acknowledgement receipt for your records.

Note: GSTR-1 must typically be filed by the 11th of the following month for monthly filers. For those under the QRMP scheme, GSTR-3B is due on the 22nd or 24th of the month, depending on your state. It’s important to always cross-check these deadlines with the latest updates from CBIC to avoid penalties or non-compliance.

GSTR-3B is where you declare your overall tax liability and claim Input Tax Credit (ITC). This is a vital part of how to file an e-commerce GST return.

Understand the Auto-populated Data in GSTR-3B

Once you file your GSTR-1, some data in GSTR-3B (like your outward supply liability) will auto-populate. More importantly, your eligible Input Tax Credit will largely be auto-populated in GSTR-2B, which helps you in filling GSTR-3B. Always compare the auto-populated data with your records.

Declaring Your Tax Liability on Sales and Reverse Charge

In GSTR-3B, you summarise your total sales for the month/quarter and calculate the GST payable on them. Also, if you have received any supplies on which the reverse charge mechanism applies, you must declare that liability here.

How to Claim Input Tax Credit (ITC) on Expenses and TCS?

This is where you reduce your tax burden. You claim ITC on the GST you paid on your business expenses, like purchases of goods for resale, packaging materials, logistics services, advertising, and other operational costs. Importantly, the Tax Collected at Source (TCS) by e-commerce operators is not claimed as Input Tax Credit (ITC). Instead, it is credited directly to your Electronic Cash Ledger, which you can then use to pay your GST liability or claim a refund. This is an essential part of the e-commerce GST file.

Making the GST Payment and Filing the Final Return

After declaring your sales, claiming ITC, and adjusting for TCS, if there is any balance tax payable, you must pay it through the electronic cash ledger. Once the payment is made, you can file your GSTR-3B using EVC or DSC. This completes the GSTR-3B filing process for the tax period.

GSTR-8 is a monthly statement filed by e-commerce operators and is mandatory for those platforms that are required to collect TCS under GST. It contains details of the supplies made through their platform and the TCS on those supplies from the sellers. As an e-commerce seller, you don’t file GSTR-8; the marketplace does.

How Does Data from GSTR-8 Help You Claim TCS Credit?

The data from GSTR-8 filed by the e-commerce operator is crucial for you. The TCS amount they collect on your sales is reflected in your GSTR-2A and GSTR-2B, and also in your electronic cash ledger on the GST portal. You can then use this balance in your electronic cash ledger to pay your GST liability or claim it as a refund, effectively receiving credit for the TCS.

Reconciling Your Sales with the Operator’s GSTR-8 Data

It’s vital to regularly reconcile your sales data with the TCS information provided by the e-commerce operators in their GSTR-8. Mismatches can lead to issues in claiming your TCS credit. The GST portal allows you to view the TCS details reported by operators, which you should cross-verify with your sales records. This reconciliation is paramount for accurate GST return filing for e-commerce.

Mismatches between your GSTR-1 and the recipient’s GSTR-2B can raise red flags with tax authorities. Discrepancies with the e-commerce operator’s GSTR-8 may also lead to the denial of Input Tax Credit.

Such errors can also lead to penalties, making incorrect GST filing in e-commerce very costly. Ignoring GST compliance altogether can lead to serious financial repercussions for your e-commerce business.

Note: Penalty limits and late fees may vary for NIL filers and small taxpayers following CBIC notifications. Always check the latest updates on cbic-gst.gov.in.

Navigating these penalties can be challenging. To ensure you remain compliant and avoid costly errors, consider connecting with a GST expert.

Can Your GST Registration be Cancelled for Non-Filing?

Yes, repeated non-filing of GST returns can lead to the cancellation of your GST registration by the tax authorities. If your GSTIN is cancelled, you will not be able to issue taxable invoices, claim ITC, or conduct taxable supplies, effectively halting your e-commerce operations. This is a severe consequence for any e-commerce seller’s GST filing.