Shopify GST Setup for Indian Stores: 2026 Step-by-Step

GST configuration in Shopify is the single most missed step in Indian store launches. A store without correct GST setup is a store that cannot legally invoice B2B customers, cannot reclaim input tax credit, and ends up with a finance team manually generating invoices in Excel. Here is how to set up GST correctly the first time.

Step 1: Add your GSTIN in Settings → Taxes

In Shopify admin, go to Settings → Taxes and duties → India. Add your GSTIN. Shopify automatically detects whether it is a regular or composition scheme registration and applies the right tax behavior.

If your store ships to multiple states, this also unlocks IGST handling for inter-state shipments and CGST+SGST for intra-state. You do not need a separate plugin for this — Shopify handles it natively in 2026.

Step 2: Configure HSN/SAC codes per product

Every product needs an HSN code (for goods) or SAC code (for services). Add it under each product → Inventory → HS code field. This is what gets printed on the invoice and what the GST system uses to calculate the right rate.

Common rates: 5 percent for handicrafts and basic apparel, 12 percent for processed food, 18 percent for electronics and most services, 28 percent for luxury goods.

Step 3: Set up GST-compliant invoice template

Shopify's default invoice template is not GST-compliant out of the box. You need a customized template that shows: GSTIN of seller, GSTIN of buyer (B2B), HSN/SAC, taxable value, CGST/SGST/IGST split, place of supply, and invoice number with a sequential prefix.

Custom invoice templates are part of our Rs. 6,600 payment gateway + invoice setup service. You can also use apps like Sufio or Order Printer with templates designed for India.

Step 4: Inter-state vs intra-state logic

Shopify auto-detects place of supply based on the shipping address. If the customer state matches your origin state, Shopify charges CGST + SGST (split equally). If different, IGST (single rate).

Pin code mismatches are the most common reason for incorrect tax. If you find tax errors after launch, audit the customer addresses first — bad address data is usually the cause.

Step 5: GSTR filing — what Shopify does and does not do

Shopify generates the data; it does not file your GSTR returns. You still need a CA or a GST filing tool (ClearTax, Zoho Books) to pull Shopify's monthly export and file GSTR-1 and GSTR-3B.

Most stores do this monthly. Set a recurring reminder or hire a CA on retainer at Rs. 3,000 to Rs. 5,000 per month.