What are the disadvantages of Shopify?

The costs stack up. On top of the monthly plan (roughly $29 Basic, $79 Shopify, $299 Advanced), Shopify charges a transaction fee when you don't use Shopify Payments — about 2% on Basic, 1% on Shopify, and 0.5% on Advanced. Since Shopify Payments isn't offered in India, Indian stores use a gateway like Razorpay and pay that extra Shopify fee plus the gateway's own card charges. Premium themes and paid apps for features Shopify lacks out of the box add more each month.

Flexibility is limited by design. Themes use Shopify's Liquid templating, so deep custom layouts and logic are harder than on a custom stack. The checkout is locked down unless you're on Shopify Plus, and the URL structure (/collections/, /products/) can't be fully changed, which constrains some SEO choices. You also depend on third-party apps for many features, and those apps can conflict, slow the store, or disappear.

Custom is better when the maths or the requirements outgrow the platform. At high order volume, per-sale fees become real money that a custom store on your own gateway avoids. Custom also wins when you need unusual B2B or subscription workflows, deep integrations with your own systems, full control over checkout and design, or complete data ownership. For a standard store that fits its model, though, Shopify still wins on speed to launch and low maintenance — the disadvantages matter most as you scale or get specific.