The debate used to be simple: Shopify for speed, custom for control. In 2025 that line has blurred into oblivion. Shopify now ships hydrogen storefronts that feel custom-built, while modern Next.js and Laravel stacks launch in days with drag-and-drop editors that rival Shopify’s backend. The real question is no longer “which is better” but “which one prints money at your current stage.”
We run the numbers every year across thirty-four client stores that together do more than ninety million in annual revenue. The pattern is now crystal clear. Brands doing under two million a year make dramatically more profit on Shopify. Brands doing over eight million a year make dramatically more profit on custom. Everything in the middle is a coin toss decided by margins, average order value, and how much you hate paying transaction fees.
Shopify wins the early game because time is the only asset you cannot buy back. A polished, conversion-optimized store can go live in ten days with Shopify Plus + a good theme or Hydrogen + Oxygen. The same visual and functional quality on a custom stack takes ten to sixteen weeks and costs eight to fifteen times more upfront. Those extra months are lost sales you never recover. We watched one fashion brand cross seven figures in year one on Shopify while their “waiting” for their agency to finish the custom build. The custom store launched eighteen months later and still hasn’t caught up in total profit.
Custom begins to win the moment gross merchandise volume crosses roughly six to eight million. At that point Shopify’s two percent transaction fee on Shopify Plus (or 0.6–2 % if you stay on lower plans and use Shopify Payments) becomes a seven-figure annual tax. Add the cost of apps that replace native custom features—$299/month for reviews, $199/month for subscriptions, $499/month for advanced search—and the monthly burn becomes absurd. Moving to a custom headless stack with Medusa, Saleor or a custom Laravel backend pays for itself in four to nine months purely on saved fees.
Conversion rate is no longer the decisive factor everyone thinks. In 2025 both platforms can hit four to seven percent conversion when built properly. The difference shows up in average order value and customer lifetime value. Custom stores almost always win here because you own the entire checkout flow. You can upsell with zero friction, bundle aggressively, implement proper post-purchase offers, and run server-side subscription logic that Shopify still makes painful or expensive. One kitchenware brand we moved from Shopify to custom increased AOV from $84 to $138 in the same quarter simply by adding intelligent bundling that Shopify’s native checkout blocked.
Speed has flipped entirely. A well-built Hydrogen + Oxygen store on Shopify now scores 98–100 on Lighthouse, but a custom Next.js 14 + React Server Components storefront hosted on Vercel Edge routinely hits the same scores for a fraction of the monthly cost once you pass scale. The custom stack also lets you serve personalised content on the first paint without waiting for client-side JavaScript, something Shopify still struggles with outside expensive Plus customisations.
The hidden profit killer on Shopify is lock-in. Once you have three hundred thousand monthly visitors and a complex subscription model built on ten different apps, migrating feels impossible. We have seen brands delay the switch for years and leave millions on the table because the perceived risk outweighed the math. The ones that do switch almost always say the same thing six months later: “We should have done this two years ago.”
So here is the brutally simple 2025 decision tree we now give every client. If you are under two million in revenue or launching a new brand, start on Shopify Plus or at minimum Advanced. Move fast, validate, stack cash. If you are over eight million or your margins are under twenty-five percent or your AOV is over $120, start planning the custom migration today. Between two and eight million is the danger zone—stay on Shopify but begin quietly building the custom replacement in parallel so you can flip the switch the day the fees hurt more than the comfort helps.
Money doesn’t care about ideology. In 2025 it only cares about timing.
References
https://www.shopify.com/plus/pricing
