Annual Compliance for E-Commerce Companies in India

Last Updated on August 14, 2026

Run a regular services business and your annual compliance is fairly predictable: ROC filings, GST returns, income tax done. Run an e-commerce business, and that same list gets a whole second layer bolted on: TCS reconciliation, a grievance officer with a 48-hour clock on every complaint, data protection obligations, and product labelling rules, sometimes even BIS or FSSAI depending on what you’re selling.

This guide walks through everything an e-commerce company in India needs to stay on top of every year, and where obligations actually differ depending on whether you’re selling through a marketplace or running your own website.

What Counts as an E-Commerce Company Here

There’s a real legal distinction worth knowing first. An e-commerce operator, under Section 2(45) of the CGST Act, is anyone who owns or runs the digital platform itself- think Amazon, Flipkart, or your own marketplace if you’re building one. If you simply sell your own products on your own website, you’re a supplier, not an operator, and that difference changes which obligations land squarely on you versus which ones the platform handles.

Selling on Amazon or Flipkart? Understand your GST registration requirements. Read our guide: GST Registration for E-Commerce Sellers on Amazon & Flipkart.

Note: if your e-commerce entity has foreign investment, DPIIT’s Press Note 2 (2018) restricts 100% FDI to the marketplace model only; an FDI-funded platform generally can’t control inventory or sell to consumers directly, only facilitate third-party sellers. This distinction shapes both business model and compliance structure from the start.

Why This Compliance Load Feels Heavier

A regular company’s obligations mostly kick in based on turnover or profit. E-commerce compliance doesn’t work that way; GST registration applies from your first sale regardless of revenue, and consumer protection obligations apply the moment you’re taking orders online, not once you hit some threshold. The rules are built around the nature of the business, not its size.

Who This Applies To

• Sellers listing products on Amazon, Flipkart, Meesho, or similar marketplaces
• D2C brands running their own website with payment gateway integration
• Platform owners operating their own marketplace connecting third-party sellers to buyers
• If you’re shipping directly to international customers (cross-border D2C, not just domestic marketplace selling), you’ll also need an Import Export Code (IEC), a one-time registration separate from GST.

The Annual Compliance Checklist for E-Commerce Business

The GST and TCS Mechanics Worth Understanding

If you’re an operator running the platform, you collect TCS at 0.5 percent on the net value of taxable supplies made through it, a rate halved from 1 percent back in July 2024, and you file GSTR-8 by the 10th of the following month. If you’re a seller on someone else’s marketplace, that TCS gets collected from your proceeds automatically, and you reconcile it against your own GSTR-1 and GSTR-3B, claiming it as credit. Getting either side wrong is a fast route to blocked credit and a notice.

If you store inventory in a marketplace’s fulfilment warehouse (e.g., Amazon FBA) located in a state where you’re not otherwise registered, that warehouse generally needs to be added as an additional place of business under your GST registration, a step sellers frequently miss until a mismatch surfaces.

Need to update your GST business locations? Read our guide: How to Add or Remove an Additional Place of Business in GST Registration.

Composition Scheme Availability for E-Commerce Sellers

Sellers making intra-state supplies through an e-commerce operator can also opt for the GST Composition Scheme (turnover up to ₹1.5 crore for goods, ₹50 lakh for services), paying tax at a flat rate instead of standard slabs. This wasn’t allowed for online sellers before 2023 and is a genuine cost-reduction option many small D2C/marketplace sellers miss.

What the Consumer Protection Rules Actually Require

Under the Consumer Protection (E-Commerce) Rules, 2020, every marketplace and inventory-model platform has to display complete seller details, name, address, contact, and GSTIN, Refunds for cancelled/returned orders should follow the timeline stated in the platform’s own refund policy the Rules require this policy to be clearly displayed, though they don’t fix a single universal number of days., and appoint a Grievance Officer whose contact details are published prominently, typically on a dedicated grievance page. Complaints need acknowledgement within 48 hours. Price manipulation and other unfair trade practices are explicitly prohibited, and in 2026, the CCPA has been actively going after newer problems too: fake reviews, deceptive subscription patterns, and deepfaked product listings.

Extended Producer Responsibility (EPR) for Plastic Packaging

If your product ships in plastic packaging, you’re likely a “Producer, Importer, or Brand Owner” (PIBO) under the Plastic Waste Management Rules and must register on the CPCB EPR portal, meet annual recycling/collection targets by plastic category, and file returns. Since July 2025, packaging must also carry a QR/barcode linked to the EPR registration number. CPCB has been actively issuing high-value penalty notices in 2026 for non-compliance; there’s no turnover exemption. This applies squarely to D2C brands and marketplace sellers shipping their own packaged products, not just large manufacturers.

Running an e-commerce store or D2C brand in India? Explore the benefits of MSME registration. Read our guide: MSME Registration for E-Commerce Sellers and D2C Brands in India.

Documents You’ll Need to Keep Current

• GST registration certificate and monthly TCS/TDS reconciliation records
• Grievance Officer appointment letter, with contact details published on the website
• A DPDP-compliant privacy policy, along with records of user consent where collected
• Under CERT-In’s 2022 directions, certain cybersecurity incidents (data breaches, unauthorised access) must be reported to CERT-In within 6 hours of detection a tight window that catches most e-commerce businesses off guard since it’s far shorter than DPDP’s own breach-notification timelines.
• Product labelling records confirming Legal Metrology compliance for packaged goods

Need help pulling this documentation together? Our experts can assist you.

Fees / Cost

There’s no separate government fee for most of these e-commerce-specific obligations; GST registration, TCS/TDS compliance, and the consumer protection requirements don’t carry standalone charges. The real cost sits in professional fees for ongoing reconciliation, since monthly TCS and TDS tracking across multiple marketplaces adds genuine bookkeeping work a standard services business simply doesn’t have.

Timeline

What’s Changed Recently

Both TCS and TDS rates for e-commerce got meaningfully lighter through 2024; TCS under Section 52 dropped from 1 percent to 0.5 percent from July that year, and TDS under Section 194-O fell from 1 percent to 0.1 percent from October. Going into 2026, the department has also leaned harder into automated GSTIN verification, flagging cases where an operator collects TCS from a seller whose registration isn’t actually valid, which means platform owners now carry real pressure to verify every vendor’s GSTIN before letting them list.

Penalty / Consequences

• Legal: Operating without GST registration attracts a penalty of 100 percent of the tax due, or a fixed minimum, whichever is higher
• Financial: Incorrect TCS or TDS reconciliation triggers interest and can block input tax credit for the seller
• Business: Missing the 48-hour grievance response window risks penalties under consumer protection law

Avoid these gaps with a properly structured e-commerce compliance calendar.

Where Companies Usually Slip Up

• Assuming the marketplace’s compliance covers the seller too, when GST and reconciliation still sit with the seller
• Publishing no grievance officer details at all, or burying them somewhere nobody would find them
• Skipping Legal Metrology labelling checks on packaged products, assuming online sales are exempt

Why Staying on Top of This Pays Off

• Keeps TCS and TDS credits flowing cleanly instead of getting stuck in reconciliation disputes
• Reduces exposure to CCPA action, which has grown noticeably more active in 2026
• Builds buyer trust through visible, functioning grievance and refund processes

A Scenario Worth Knowing About

A D2C skincare brand launches its own website alongside an Amazon storefront, assuming the same compliance effort covers both. On Amazon, the platform handles seller display and part of the grievance process. On the brand’s own site, none of that exists by default: no visible grievance officer, no formal privacy policy, no refund timeline stated anywhere. A customer complaint escalates to the National Consumer Helpline, and the brand only then realises its own website was never brought up to the same standard Amazon enforced automatically.

A Few Things Worth Doing Differently

• Treat your own website’s compliance as a separate checklist from your marketplace listings
• Reconcile TCS and TDS every month, not just when preparing the annual return
• Review your privacy policy and grievance process at least once a year, not just at launch

Marketplace Seller vs Own D2C Website: Who’s Responsible for What

How Kanakkupillai Can Help

We handle annual ROC compliance alongside the e-commerce-specific layer, GST and TCS reconciliation, grievance officer setup, DPDP-compliant policies, and Legal Metrology checks, so whether you’re selling through a marketplace, your own site, or both, nothing falls through the cracks.

Conclusion

E-commerce compliance in India isn’t just standard company compliance with a few extra forms; it’s a genuinely different load, built around turnover-independent GST registration, monthly TCS and TDS reconciliation, and consumer protection obligations that apply from your very first sale. Knowing exactly which of these sit with you versus the platform is what keeps a growing e-commerce business from discovering a gap the hard way. Get expert help with your e-commerce company’s annual compliance from Kanakkupillai today.

FAQs

1. Do I need GST registration if I only sell a few products a month online?

Yes, GST registration is mandatory for anyone selling through an e-commerce platform, regardless of turnover. The usual Rs. 20 lakh or Rs. 40 lakh exemption thresholds simply don’t apply to online sellers. This is true for most e-commerce sellers, but small intra-state sellers of goods can operate without full GST registration using an enrolment number instead if turnover stays within the standard threshold, they don’t sell inter-state, and they operate in only one state (Notification No. 34/2023, effective October 2023).

Under the enrolment route, sellers get a unique enrolment number (not a full GSTIN) valid only for the specific platform and state declared; switching to inter-state sales or a second platform state requires full registration.

2. What’s the difference between TCS under Section 52 and TDS under Section 194-O?

TCS under Section 52 is a GST provision, where the operator collects 0.5 percent and remits it against the seller’s GST liability. TDS under Section 194-O is an income tax provision, where the operator deducts 0.1 percent against the seller’s income tax liability. They apply in parallel, not instead of each other.

3. Do I need a Grievance Officer if I only sell through Amazon or Flipkart?

The marketplace typically handles much of this on its platform, but if you also run your own website or app for direct sales, you need your own Grievance Officer and display requirements there, independent of what the marketplace provides.

4. Does the DPDP Act apply to a small e-commerce business?

Yes, the DPDP Act applies to any business processing personal data, including customer names, addresses, and payment details, regardless of company size. A privacy policy and basic consent management are expected from the outset.

5. Are Legal Metrology labelling rules different for products sold online versus in stores?

No, the same MRP, net quantity, and manufacturing details required on physical packaging apply to products sold online. The rules don’t create an exemption just because the sale happens through a website or app.

6. What happens if TCS collected doesn’t match what I report in my GST returns?

This mismatch typically shows up during reconciliation and can delay or block your input tax credit claim, along with inviting a notice from the department asking you to explain the gap.