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Published on:

May 16, 2025

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Compliances for E-Commerce Operators and Participants Under GST and Income Tax

Compliance for E-Commerce Operators and Participants Under GST and Income Tax

The e-commerce boom in India is no secret. From daily groceries to high-end electronics, just about everything can be bought with a few taps on your screen. But behind this digital storefront lies a web of laws and compliance requirements that both e-commerce operators (like Amazon, Flipkart, Meesho) and participants (the sellers) must carefully navigate. Especially when it comes to Goods and Services Tax (GST) and Income Tax, the rules are anything but casual.

Whether you're a seller hustling to stand out in the crowded online bazaar or the platform pulling the strings behind those virtual storefronts, staying on top of tax compliance isn’t just another item on your to-do list — it’s the backbone of running a legit, stress-free operation. Slip up here, and you could be inviting a world of trouble. But don’t worry — we’re about to unpack everything in plain speak, without drowning in legal jargon.

Meet the Key Players in the E-Commerce Game

Before we dive headfirst into the tax maze, let’s get a handle on who’s who in this digital marketplace:

E-Commerce Operators (ECOs): Think of the big guns like Amazon, Flipkart, and Snapdeal — these are the folks running the show. If you’re hosting or managing a digital platform where buyers and sellers do business, congratulations, you’re officially an ECO in the eyes of the law.

E-Commerce Participants/Sellers: These are individuals or businesses that list their products or services on the above platforms.

GST Compliance for E-Commerce Operators

1. Mandatory GST Registration

First things first — registration is non-negotiable. Regardless of turnover, e-commerce operators must register under GST. No threshold exemption applies here. Even if your revenue is zero today, the law doesn’t care. You still need a GSTIN.

For sellers too, GST registration is mandatory if they supply goods through an e-commerce platform — again, regardless of turnover. Service providers, on the other hand, may get threshold exemption, but there are nuances.

2. TCS (Tax Collected at Source) Obligations

Now here’s where things get a little spicy. E-commerce platforms aren’t just middlemen — they’ve got tax duties too. Under GST rules, they’re required to collect Tax Collected at Source (TCS) at 1% on the net taxable value of supplies made through their site. That breaks down to 0.5% CGST and 0.5% SGST, or 1% IGST, depending on where the goods are going. In short, for every sale happening on the platform, the taxman wants a tiny slice — and the platform has to collect it.

So, let’s say a seller earns ₹1,00,000 through Amazon in a month, excluding returns and cancellations. Amazon is required to collect ₹1,000 (1%) as TCS and remit it to the government.

This TCS amount shows up in the seller's GST portal and can be claimed as credit while filing returns. It's not a loss — just an advance payment, in a sense.

3. Monthly and Annual GST Returns

ECOs have to file a separate return — GSTR-8, which captures all the TCS details. This is in addition to their regular GSTR-1 and GSTR-3B filings.

Sellers, on the other hand, must file GSTR-1 and GSTR-3B regularly. The TCS details auto-populate in their return dashboard, making reconciliation a tad easier — in theory, at least.

4. Invoice and Reporting Norms

Every transaction must be supported with proper GST-compliant invoices. No shortcuts here. Each invoice must mention the seller’s GSTIN, HSN/SAC code, applicable tax rate, and the value of goods/services.

For ECOs, maintaining digital logs and transaction history is not just best practice — it’s a compliance necessity. In the event of scrutiny, you don’t want to be scrambling through spreadsheets at 2 a.m.

GST Compliance Challenges for Sellers

Mismatch of Returns: If the TCS collected by the platform doesn’t match what the seller reports, expect a notice. These mismatches are common, especially with returns, refunds, and bulk discounts.

State-wise Registration: If a seller delivers to multiple states directly (not via a central warehouse), they may be required to take state-wise GST registrations — a logistical headache for small businesses.

Reverse Charge Mechanism (RCM): Sellers availing services like delivery or warehousing from the ECO may attract RCM liability in some cases.

Income Tax Compliance for E-Commerce Participants

GST isn’t the only watchdog around. The Income Tax Department has its own checklist.

1. Income Disclosure

All earnings through online platforms are taxable. Whether you’re an individual seller making side income or a registered company, you must declare the full income in your ITR.

Now, the catch is — even if the platform has already deducted TDS (we’ll get to that), you still need to report the gross income, not the net amount received in your bank account.

2. TDS Under Section 194-O

Let’s not forget the Income Tax side of the story. Starting from FY 2020-21, a new rule — Section 194-O — made its debut. It requires platforms like Amazon or Flipkart to deduct 1% TDS before paying sellers. But there’s a twist: this only kicks in if your annual sales cross ₹5 lakh, and you haven’t provided your PAN or Aadhaar. Hit that threshold without proper paperwork, and the platform starts snipping a bit off the top before your earnings even reach you.

Even for small sellers, this means a portion of their revenue is being withheld, and they’ll need to claim it as TDS credit in their income tax returns.

3. Filing the Right ITR

If you’re an individual seller, you’ll likely file ITR-3 (for business income) or ITR-4 (under presumptive taxation). For companies or LLPs, it’s ITR-5 or ITR-6, depending on the entity type.

Choosing the wrong ITR form can be costly, both in terms of penalties and mental peace.

4. Books of Accounts

Maintaining books of accounts isn't optional if your turnover exceeds the prescribed limits. Even if you're under presumptive taxation, keeping a record of invoices, payments, returns, and commissions paid to platforms is critical.

Because, come audit season, you don’t want to be digging through email receipts like you’re on a treasure hunt.

Additional Compliance Burdens to Watch

1. Audit Requirements

If your turnover crosses ₹1 crore (or ₹10 crore for digital transactions), an audit under Section 44AB of the Income Tax Act may apply. And that’s a whole new world of paperwork.

2. Advance Tax

Got decent monthly sales? Don’t wait till March. You may need to pay advance tax in quarterly installments. Missing these can attract interest under Sections 234B and 234C.

3. Reconciling with Platform Data

Platforms like Amazon and Flipkart generate reports for each seller. It’s essential to cross-check your financial records with their transaction reports, including:

Gross sales

TCS & TDS details

Shipping charges

Discounts and returns

Any mismatch, and the taxman might come knocking.

Penalties and Pitfalls

Failing to comply isn’t just risky — it can burn a hole in your pocket:

Late fees under GST for delayed returns

Interest on unpaid taxes

Penalties for non-registration

Scrutiny under income tax for under-reporting

The worst part? Most of these issues arise not from intentional fraud but from sheer negligence or misunderstanding of the rules.

Tips to Stay on Top of Compliance

Here are some real-world tips to keep your e-commerce business squeaky clean (at least from a tax perspective):

Automate your invoicing: Use software that’s GST-compliant and integrates with your e-commerce platform.

File returns on time: Mark calendar reminders or use a CA who’s on their toes.

Reconcile monthly: Don’t wait till year-end to fix discrepancies

Keep digital backups: Cloud storage is your best friend.

Hire a professional: If compliance makes your head spin, get a tax consultant who knows the e-commerce game.

Wrapping Up

Selling online can be a thrilling ride, but it’s not all glitter and glam. With great visibility comes great responsibility — especially when it comes to taxes. Whether you’re just starting out or already running a multi-crore storefront, staying on top of GST and income tax compliance is non-negotiable.

Remember, it’s better to spend a few hours getting your books in order today than months untangling tax notices tomorrow.

FAQs

1. Do I need to register under GST even if I sell occasionally on platforms like Amazon or Flipkart?

Yes, if you’re selling goods through any e-commerce platform, GST registration is mandatory — even if your turnover is below ₹20 lakh (₹10 lakh in special category states). There’s no threshold exemption for online sellers dealing in goods.

2. What’s the difference between TCS and TDS in e-commerce?

TCS (Tax Collected at Source) is collected by the e-commerce operator under GST laws at 1% on net taxable supplies.

TDS (Tax Deducted at Source) is deducted under Income Tax laws (Section 194-O) at 1% of gross sales.

Think of TCS as a GST thing and TDS as an Income Tax thing — both get deducted, both are visible in your respective tax dashboards, and both can be claimed while filing returns.

3. What if my earnings are below ₹5 lakh in a financial year — will TDS still apply?

If your annual sales through a single e-commerce operator do not exceed ₹5 lakh, and you’ve furnished your PAN/Aadhaar, then TDS under Section 194-O will not apply. But once you cross ₹5 lakh, even by a rupee, TDS kicks in.

4. Can I claim TCS and TDS back? Are these extra taxes?

Not really “extra” — think of them as advance tax payments. The amounts deducted as TCS (under GST) and TDS (under Income Tax) can be claimed as credit in your tax returns. They reduce your final tax liability.

5. I sell digital products like eBooks and courses. Do the same rules apply?

Yes, mostly. If you're selling digital goods or services, GST still applies, and if you sell via a platform (like an aggregator), TCS obligations may arise for the platform. However, service providers may qualify for threshold exemption under GST depending on the nature of supply and platform structure. Always check with a tax consultant for specifics.

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