Selling online on Shopify, Amazon, or Flipkart? GST compliance is mandatory. This guide covers registration, invoicing, TCS, returns, and how to stay compliant without losing your mind.
If you sell products online in India, GST hits you differently than a regular shop. The rules are more complex because e-commerce involves three parties — you (the seller), the platform (Shopify, Amazon, Flipkart), and the customer who could be in any state. This creates inter-state supply situations that a local shop never faces.
The biggest complexity is TCS (Tax Collected at Source). Under Section 52 of the CGST Act, e-commerce operators like Amazon and Flipkart must collect 1% TCS on the net value of taxable supplies made through their platform. This TCS is deducted from your payout — so you receive less than the invoice value. You then claim this TCS as credit when filing GSTR-3B.
We built myBillPlease specifically to handle e-commerce GST complexity. Our Shopify integration auto-syncs orders and creates GST invoices with correct inter-state/intra-state tax splits. For marketplace sellers on Amazon and Flipkart, we are building integrations — meanwhile, you can use myBillPlease as your central billing hub. This guide covers everything you need to know about GST compliance as an online seller.
Mandatory registration — no threshold exemption. Unlike regular businesses that need GST registration only above Rs 20 lakh turnover, e-commerce sellers who supply through e-commerce operators must register regardless of turnover. Even if you sell Rs 1,000 worth of goods through Amazon, you need GST registration. This is specified under Section 24 of the CGST Act.
Exception: If you only sell through your own website (like a Shopify store without listing on marketplaces), the regular Rs 20 lakh threshold applies. But once you list on any marketplace — Amazon, Flipkart, Meesho, or others — mandatory registration kicks in.
Multi-state registration: If you store inventory in warehouses in multiple states (like Amazon FBA in Delhi, Mumbai, and Bangalore), you need GST registration in each state where you have a place of business. Each state registration files separate GSTR-1 and GSTR-3B returns.
The registration process is the same as regular GST — apply online at gst.gov.in with your PAN, Aadhaar, business documents, and bank details. Approval typically takes 3-7 working days.
The 1% deduction that confuses most online sellers
E-commerce operators collect 1% TCS (0.5% CGST + 0.5% SGST for intra-state, or 1% IGST for inter-state) on the net value of taxable supplies. This is deducted from your payout before you receive it.
Amazon, Flipkart, Meesho, and other marketplace operators deduct TCS. If you sell on your own Shopify store without a marketplace, no TCS applies — you collect and pay GST directly.
The TCS deducted appears in your electronic cash ledger on the GST portal. You claim it as credit when filing GSTR-3B. It reduces your net tax payable. If TCS exceeds your liability, you can claim a refund.
The e-commerce operator files GSTR-8 every month reporting all TCS collected. Your TCS details appear in your GSTR-2B auto-populated statement for matching and reconciliation.
TCS is on the net value — total taxable supply minus returns. If you sold Rs 1 lakh and had Rs 10,000 in returns, TCS is on Rs 90,000. The operator calculates this automatically.
TCS means your payout is 1% less than expected every month. For high-volume sellers doing Rs 10 lakh monthly, that is Rs 10,000 deducted. Plan your cash flow accordingly — the credit comes back when you file GSTR-3B.
Every online sale needs a proper GST invoice — whether the customer is a business (B2B) or individual consumer (B2C). The invoice must follow the same mandatory format rules as offline invoices — 16 mandatory fields including GSTIN, HSN codes, and tax breakup.
Inter-state vs intra-state: This is where e-commerce gets tricky. If your business is in Maharashtra and the customer is in Delhi, it is an inter-state supply — charge IGST. If both are in Maharashtra, it is intra-state — charge CGST + SGST. The determination is based on where your goods are delivered (Place of Supply), not where the customer lives.
B2B vs B2C classification: If the customer provides their GSTIN on the order, it is a B2B sale. Report it in GSTR-1 Table 4 with their GSTIN. If no GSTIN, it is B2C. Inter-state B2C above Rs 2.5 lakh goes in Table 5. Everything else is B2C Small in Table 7.
Shopify sellers: myBillPlease handles all of this automatically. When a Shopify order syncs, the system reads the delivery state, compares it with your business state, and applies the correct IGST or CGST+SGST split. The invoice generates with all mandatory fields. For marketplace sellers, you create invoices manually or import via CSV — the tax calculation logic is the same.
Monthly or quarterly filings depending on your turnover
Amazon sellers: Amazon deducts TCS and provides a monthly TCS certificate. Download it from Seller Central → Tax Documents. Reconcile with your GSTR-2B to ensure all deductions are accounted for. Amazon also generates invoices on behalf of some sellers — verify that the GSTIN, HSN codes, and tax amounts on Amazon-generated invoices are correct.
Flipkart sellers: Similar to Amazon — TCS is deducted and reported in GSTR-8. Flipkart provides tax reports in the seller dashboard. Key difference: Flipkart sometimes adjusts returns and penalties in the same payout, making reconciliation trickier. Keep a separate tracker for net payouts vs gross sales.
Shopify sellers (own store): No TCS deduction — you collect GST directly from customers. This simplifies compliance significantly. With myBillPlease's Shopify integration, orders sync automatically, invoices generate with correct tax, and GSTR reports compile themselves. This is the simplest e-commerce GST setup available.
Multi-platform sellers: If you sell on Amazon, Flipkart, and your own Shopify store, maintain one central billing system for all channels. Shopify orders sync to myBillPlease automatically. Marketplace orders you record manually or import via CSV. All invoices — across all channels — feed into one GSTR-1 and one GSTR-3B. No duplicate filing, no missed invoices.
E-commerce GST compliance does not have to be painful. The key is having one billing system that handles invoicing, tax calculation, and return generation from a single source of truth.
myBillPlease does exactly this. Shopify orders sync automatically. For other platforms, import orders via CSV. Every invoice gets the correct IGST or CGST+SGST calculation. GSTR-1 and GSTR-3B reports generate from your invoice data. TCS from marketplace operators reflects in your GSTR-2B reconciliation.
The free plan includes unlimited invoices and basic GST reports. Shopify integration and advanced reports including GSTR-2B reconciliation are in the Starter plan at Rs 799/month. See all plans or read how our e-commerce billing features work.
Shopify auto-sync, correct inter-state tax, GSTR reports on autopilot. Free plan with unlimited invoices.
Get Started Free