GST for E-Commerce Sellers — Amazon, Flipkart & Meesho Compliance Guide
By Parul Singh, GST Practitioner · GST Special · Updated June 2026
Table of Contents
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TCS by E-Commerce Operators
I manage GST compliance for 100+ e-commerce sellers in Delhi. Missing compliance means Amazon blocks your payouts. E-commerce operators (Amazon, Flipkart, Meesho, Myntra) collect Tax Collected at Source (TCS) at 1% (0.5% CGST + 0.5% SGST for intra-state; 1% IGST for inter-state) on every sale made through their platform.
Official Reference: Section 52 of the CGST Act 2017 mandates TCS collection by e-commerce operators. Rule 58 provides the procedure. The operator must collect TCS on the net value of taxable supplies (gross sales minus returns) at 1% and deposit it with the government by 10th of next month.
📍 Real Example -- Amazon Seller in Nehru Place
Rajesh sells electronics on Amazon from Nehru Place. Monthly sales: ₹5,00,000. Amazon collects: 1% TCS = ₹5,000 (₹2,500 CGST + ₹2,500 SGST). This ₹5,000 appears in Rajesh's GSTR-2A as TCS credit. He can use it to reduce his output tax liability in GSTR-3B. If he does not file returns, this ₹5,000 remains unclaimed -- and accumulates every month.
Registration Requirements for E-Commerce Sellers
- Mandatory GST registration -- No threshold exemption for e-commerce sellers under Section 24(ix)
- Even if your turnover is ₹1, you must register
- PAN-based registration -- one GSTIN per state
- Must mention marketplace GSTIN on invoices
⚠️ Common Mistake: The biggest shock for new sellers: GST registration is mandatory even below ₹20 lakh turnover. I had a client in Janakpuri selling ₹5,000/month on Meesho. She assumed the threshold applied. When Amazon requested her GSTIN for onboarding, she realized she needed to register. The good news: voluntary registration also works and builds credibility.
Return Filing for E-Commerce Sellers
- GSTR-1: Monthly by 11th -- report all marketplace sales
- GSTR-3B: Monthly by 20th -- claim TCS credit
- GSTR-8: Filed by the e-commerce operator (not you) by 10th of next month
- TCS amount auto-appears in your GSTR-2A after operator files GSTR-8
Claiming ITC on TCS Collected
The TCS collected by Amazon/Flipkart is your money -- it is a credit, not a cost. Here is how to claim it:
- Wait for the marketplace to file GSTR-8 (usually by 10th)
- Check GSTR-2A -- TCS amount should appear under "TDS/TCS Credit"
- Claim the credit in GSTR-3B Table 4
- Use it to offset your output tax liability
📍 Real Example -- Flipkart Seller Monthly Compliance
A Flipkart seller in Dwarka with ₹8 lakh monthly sales:
• Output tax on sales: ₹1,44,000 (18%)
• TCS collected by Flipkart: ₹8,000
• ITC on purchases: ₹60,000
• Net tax payable: ₹1,44,000 - ₹60,000 - ₹8,000 = ₹76,000
Without claiming TCS, he would overpay ₹8,000 every month = ₹96,000/year!
• Output tax on sales: ₹1,44,000 (18%)
• TCS collected by Flipkart: ₹8,000
• ITC on purchases: ₹60,000
• Net tax payable: ₹1,44,000 - ₹60,000 - ₹8,000 = ₹76,000
Without claiming TCS, he would overpay ₹8,000 every month = ₹96,000/year!
💡 Pro Tip from Parul: Always reconcile TCS shown in GSTR-2A with your marketplace payout reports. Amazon and Flipkart sometimes delay GSTR-8 filing or report incorrect amounts. A ₹500 monthly discrepancy can accumulate to ₹6,000/year in lost credits.
Common E-Commerce GST Mistakes
- Not registering at all -- thinking the threshold applies
- Not claiming TCS credit -- leaving free money on the table
- Wrong HSN codes -- marketplace may assign wrong rates
- Not reconciling marketplace reports with GSTR-1 -- mismatch triggers notices
- Missing the composition scheme trap -- composition dealers CANNOT sell on marketplaces
💡 Pro Tip from Parul: I specialize in e-commerce GST compliance. My package for online sellers covers registration, monthly filing, TCS reconciliation, and marketplace coordination -- all for ₹2,499/month. Call/WhatsApp: +91 95401 04776
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Frequently Asked Questions
Can composition scheme dealers sell on Amazon/Flipkart?
No. Composition taxpayers cannot supply goods through e-commerce operators. This is explicitly barred under Section 10(2)(d). If you want to sell on Amazon, you must be on the regular GST scheme.
What if Amazon/Flipkart deducts TCS but does not deposit it?
The marketplace is legally required to deposit TCS by 10th of next month and file GSTR-8. If they fail, you can raise a ticket with the marketplace and also file a grievance on gst.gov.in. Your ITC claim depends on the operator filing GSTR-8.
Do I need separate GST registration for each marketplace?
No. One GST registration covers all marketplaces. You use the same GSTIN on Amazon, Flipkart, Meesho, and your own website. However, if you have godowns in multiple states, you need separate registrations per state.
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