Shopify is the one platform in this list that already has a cost field. Add a Cost per item value to a product and the built-in Profit reports show gross profit and margin per order, right in the admin. Most Indian sellers still don't see true profit, because that field only covers COGS — it says nothing about GST split-out, courier, payment gateway fees, or what returns actually cost you. A store running healthy gross margins in the Shopify dashboard can still be down to single digits once those four lines are counted.
What Shopify's Profit reports get right — and where they stop
Once Cost per item is filled in for every variant, Shopify computes gross profit and gross margin automatically, at the order, product and variant level. That's more than OpenCart or a bare WooCommerce install give you natively. But the number Shopify shows is gross profit against the full order value — it isn't net of GST, and it doesn't touch courier cost, payment gateway charges, or a return allowance. For an India-based store those four gaps are usually where the real margin erosion happens, not in COGS.
There's also a currency problem for anyone still entering cost in USD from an old theme setup: if store currency and cost currency don't match, the margin number in the report is simply wrong. Worth checking before trusting it for pricing decisions.
The GST piece Shopify leaves to an app
Shopify's tax engine can charge the right amount — CGST plus SGST on intra-state orders, IGST across states — but it can't natively split a single order into two tax line items, so most Indian merchants set up a combined override that charges the correct total instead of a true CGST/SGST breakdown. HSN codes go into the HS tariff code field on each product (Shopify requires at least 6 digits there, so shorter codes need a metafield or tag instead). None of this produces a GST-compliant invoice — Shopify doesn't generate one natively, which is why almost every Indian Shopify store runs a GST invoicing app alongside it for HSN-tagged, CGST/SGST/IGST-split bills and GSTR-ready exports.
One thing a self-owned Shopify store doesn't have to deal with: TCS under GST Section 52. That 1% collection applies when an e-commerce operator facilitates sales for other sellers — Amazon, Flipkart, Meesho filing GSTR-8 on your behalf. A Shopify store is your own operator selling your own inventory, so there's no TCS deduction sitting between your settlement and your bank account, and no GSTR-8 reconciliation. Input tax credit on your purchases works the same way it would anywhere else.
One order, worked through
A ₹1,999 apparel item, GST-inclusive at the 18% standard rate, sold direct through a Shopify store, paid for via a third-party gateway since Shopify Payments isn't available in India.
| Line | Amount |
|---|---|
| Selling price (18% GST-inclusive) | ₹1,999 |
| Net revenue (ex-GST) | ₹1,694 |
| Purchase cost | −₹850 |
| Courier | −₹90 |
| Payment gateway fee (illustrative, ~2%) | −₹40 |
| Return allowance (8%, apparel) | −₹10 |
| True profit | ₹704 (~42% margin) |
Shopify's Profit report, fed only the ₹850 cost, would show roughly ₹1,149 gross profit on this order — a 57% margin against the ₹1,999 order value. The gap to the real 42% comes entirely from GST, courier, gateway and return costs, and none of those three show up in the native report at all.
Connecting Shopify order data to real profit numbers
Klean Profit AI takes a CSV export of your Shopify orders — something every plan supports natively — alongside your cost, courier and GST data, and computes trusted profit per SKU: net revenue ex-GST, minus purchase cost, courier, payment gateway fees and a return allowance. The same 15+ data-quality checks that catch a missing cost price or a mismatched GST rate on an OpenCart or Zoho import run on the Shopify CSV too, so a bad row gets flagged instead of quietly skewing your contribution margin. Your order and cost data is never used to train the underlying AI models. If you also list on Amazon, Flipkart or Meesho alongside your Shopify store, the same catalogue gets one profit view instead of a Shopify number and three marketplace numbers that don't reconcile.
Common mistakes Shopify sellers make
- Trusting the Profit report as final. It's gross profit against GST-inclusive revenue, not net profit — courier, gateway fees and returns aren't in it.
- Leaving Cost per item blank on new variants. Every SKU launched without it quietly reports 100% margin until someone notices.
- Ignoring the payment gateway fee. With Shopify Payments unavailable in India, every order carries a third-party gateway charge that eats into margin the same way a marketplace commission does.
- Not separating GMV from net settlement. Gross sales, GST collected and what actually lands in the bank are three different numbers — pricing off the first one overstates what you keep.
Does Shopify calculate profit per product?
Yes, at a basic level — fill in Cost per item and the built-in Profit reports show gross profit and margin per order, product and variant. It's gross against GST-inclusive revenue, though, so it doesn't net out courier, payment gateway fees or returns.
How do I charge CGST, SGST and IGST correctly on Shopify?
Shopify can't split one order into two tax line items natively, so most Indian stores set a combined tax override that charges the correct CGST+SGST or IGST total based on the buyer's state, then rely on a GST invoicing app to show the compliant breakdown and HSN codes on the actual invoice.
Does TCS under GST apply to my own Shopify store?
No. TCS under Section 52 applies when an e-commerce operator collects payment on behalf of other sellers and files GSTR-8 — that's Amazon, Flipkart or Meesho's obligation for marketplace sellers. A Shopify store is your own operator selling your own stock, so there's no TCS deduction in your settlement.
Why does my Shopify Profit report show a higher margin than my bank balance suggests?
The report is gross profit against a GST-inclusive selling price, calculated only from Cost per item. GST owed to the government, the courier cost, your payment gateway's cut and a fair share of returns all come out after that number is shown — which is usually most of the gap.
Can I see combined profit across Shopify and marketplace channels?
Not from Shopify's own reports — those cover Shopify orders only. Pulling Shopify, Amazon, Flipkart and Meesho data into one profit-per-SKU calculation is what shows whether a product is actually worth stocking across every channel it sells on, not just the one you happened to check.