Your Shopify Fees Just Hit $24,000 This Year. Here's Your Exit.

A DTC brand doing $800,000 in annual revenue on Shopify's Basic plan at 2.9% + 30¢ per transaction can expect to hand over roughly $24,000 a year in payment processing fees alone -- before apps, theme costs, or the subscription itself. Moving from Shopify to MedusaJS eliminates the platform's transaction surcharge entirely, because Medusa is open-source software with no per-sale fee. You still pay your payment processor (Stripe, for example, charges its own rates), but you stop paying Shopify's markup on top of that.

We have migrated stores off Shopify, off WooCommerce, off Sitecore. The pattern is always the same: the operator hits a cost or control ceiling and needs a way out that does not mean starting from scratch. I remember one founder pulling up her Shopify invoice during our first call, pointing at a $1,400 app stack she had cobbled together over three years, and saying, "I don't even know what half of these do anymore." That is the moment people start looking. This page lays out exactly what the Shopify-to-MedusaJS path looks like -- scope, cost, timeline, and the honest trade-offs.

How much does Shopify actually cost a high-volume DTC brand?

Shopify's published plans range from $29/month (Basic, annual) to $2,500/month (Plus). But the subscription is the smallest line item. According to Shopify's own developer documentation, third-party payment providers incur an additional transaction fee of 2% on Basic, 1% on Shopify, and 0.6% on Advanced -- layered on top of whatever your gateway charges. Even if you use Shopify Payments to avoid that surcharge, credit card rates still sit at 2.9% + 30¢ on Basic.

Research from a detailed 2026 cost analysis by Matija (an agency owner building mid-market commerce with Medusa and Next.js) puts Shopify's initial costs between $34,400 and $72,000 depending on plan and complexity -- factoring in subscriptions, design, apps, transaction fees, email, tax tools, and marketplace connectors. That same analysis found Medusa's initial costs can be up to 39% lower, because there is no platform license and no GMV-based fee.

Here is the real math most operators miss:

• Shopify Basic at $800K GMV: ~$23,200 in card processing (2.9%) + ~$2,400 in per-transaction fees (30¢ x ~8,000 orders) + $348 annual subscription = roughly $26,000/year before apps.
• Medusa + Stripe at $800K GMV: ~$23,200 in Stripe processing (2.9%) + ~$2,400 in per-transaction fees (30¢ x ~8,000 orders) + $0 platform fee + $50-$200/month hosting = roughly $26,000-$28,000/year.

The processing cost stays similar because Stripe's rates are comparable. Where the savings actually show up is everything Shopify charges beyond processing: subscription tier upgrades that become inevitable as you scale, app subscriptions ($200-$800/month is normal for a mature store), and the 2% third-party gateway fee if you choose not to use Shopify Payments. A brand at $2M GMV on Shopify Advanced pays $2,388/year just for the plan, plus apps, plus fees. On Medusa, your costs grow with engineering and infrastructure, not with revenue.

When should you choose MedusaJS over Shopify?

Not always. We are opinionated about this because we have watched both sides go sideways.

Shopify is the right call when a team wants to launch fast, does not have in-house engineering, and is under $500K in annual revenue. Shopify's app ecosystem -- over 16,000 apps -- handles most standard needs without writing code. If your business model fits Shopify's rails, stay on them. Seriously.

MedusaJS makes sense when:

• You need custom checkout logic. Shopify locks checkout customization behind the $2,500/month Plus plan. Medusa's checkout is yours to build from the ground up.
• You run multi-region, multi-currency operations with pricing rules more complex than what three B2B catalogs can handle.
• You are building a composable stack where your commerce engine is one piece alongside a headless CMS, a custom ERP connector, or marketplace logic no Shopify app covers.
• You refuse platform lock-in. You want to own your data, your code, and your deployment. Full stop.
• Your transaction volume makes Shopify's fee structure punitive. At $3M+ GMV, the compounding cost of Shopify's layered fees versus owning your infrastructure becomes hard to ignore.

For a broader comparison of Shopify's limits versus headless alternatives, we wrote a detailed breakdown in Your WooCommerce Store Just Hit the Wall. Here's Your Exit. that covers the architectural argument for going headless.

What does MedusaJS actually give you out of the box?

Medusa is an open-source Node.js commerce engine. It is not a website builder. It is the backend that handles the business logic -- products, orders, inventory, customers, discounts, gift cards, tax calculation, multi-currency, multi-region -- and exposes it all through a REST API and JS SDK.

What ships with Medusa v2:

• Admin dashboard -- built-in, functional, extensible.
• Payment integrations -- Stripe, PayPal, and a plugin architecture for anything else.
• Multi-region and multi-currency -- native, not bolted on.
• Modular architecture -- swap out modules (fulfillment, payment, notification) without touching the rest.
• No transaction fees, no revenue share, no platform license.

What Medusa does not give you: managed hosting, one-click themes, a plug-and-play app store, or 24/7 support chat. You bring your own frontend (typically Next.js), your own hosting (Railway, AWS, DigitalOcean -- typically $20-$200/month depending on scale), and your own engineering capacity or an agency that knows the stack.

The Growww Tech comparison from 2026 puts it plainly: "For teams with real engineering capability -- yes, Medusa v2 is production-ready. For solo non-technical founders -- no."

I could not agree more. This is not a platform you hand to a marketing team and walk away from. It is a platform you build on when you need something no SaaS will give you.

What does the migration from Shopify to MedusaJS actually involve?

We have done this enough times to give you a reliable scope. A typical Shopify-to-MedusaJS migration for a DTC brand with 500-5,000 SKUs, a few years of order history, and an active customer base follows this sequence:

1. Data export and transformation (Week 1-2). Products, variants, customers, historical orders, collections, discount codes, and gift card balances come out of Shopify's Admin API. We transform the data into Medusa's schema and import it into a staging instance. This step always takes longer than people expect because Shopify's data export is messier than it looks from the outside.
2. Storefront rebuild (Week 2-6). The frontend is built in Next.js using your existing design language. This is not a template -- it is a custom build that matches (or improves) what you had on Shopify.
3. Checkout and payment integration (Week 4-6). Custom checkout flow wired to Stripe (or your preferred processor). No Shopify Payments dependency. You negotiate your own rates directly with your processor.
4. SEO and redirect mapping (Week 5-7). Every existing URL gets a 301 redirect. We map collection pages, product URLs, and blog posts. Losing SEO equity during a migration is the most common -- and most avoidable -- mistake. I have personally watched a brand lose 40% of organic traffic because someone forgot to map their /collections/ URLs. That was not our project, but we cleaned it up afterward.
5. QA, load testing, DNS cutover (Week 7-8). DNS switches with zero downtime using a blue-green deployment pattern.

Total timeline: 6-10 weeks for a standard DTC catalog. Complex B2B or multi-region setups push that to 10-14 weeks. For a deeper look at platform cost comparisons and the decision framework, see Your Shopify Bill Just Hit $2,000/mo. Is Medusa.js Your Exit?.

What are the honest trade-offs of leaving Shopify?

We would not be worth hiring if we did not tell you what you lose.

• App ecosystem. Shopify's 16,000+ apps mean you can add loyalty programs, reviews, subscriptions, and upsells in minutes. On Medusa, most of those integrations are custom development. Budget accordingly.
• Maintenance responsibility. Security patches, server scaling, database backups, uptime monitoring -- all yours. On Shopify, that is their problem.
• Longer initial development time. A Shopify store can launch in days. A Medusa build takes weeks to months. If speed to market is your primary constraint, this matters a lot.
• Smaller community. Medusa's ecosystem is growing but is still small relative to Shopify. Some integrations require forking community plugins or building from scratch.

These are real costs. We have seen brands migrate to open-source and completely underestimate the operational load. If you do not have at least one senior developer on staff -- or a retained agency relationship -- the ongoing maintenance will eat whatever you saved on transaction fees. I watched a three-person team try to self-manage a Medusa instance without dedicated dev support. Within four months they were back on Shopify. That is not a knock on Medusa; it is a knock on underestimating what "you own the infrastructure" actually means week after week.

For brands evaluating other escape routes from expensive platforms, we have written similar migration guides: Your Sitecore Renewal Invoice Just Hit Your Inbox. Here's Your Exit Plan. covers enterprise CMS exits, Your Second Market Just Broke Shopify. Here's Your Exit. walks through the Saleor alternative, and Your Teachable Bill Just Hit $1,847/Month. Here's Your Exit Plan. addresses course platform migrations.

The real question is not about the platform -- it is about ownership

Every platform decision is a bet on where you want complexity to live. Shopify puts complexity behind a monthly bill and a percentage of your revenue. Medusa puts it in your codebase and your team's hands. Neither is wrong.

One is cheaper at scale if you have the engineering discipline to maintain it. The other is cheaper at launch if you value speed and simplicity over control. That is the whole decision, honestly.

The brands we have migrated from Shopify to MedusaJS share a common profile: $1M+ in GMV, a technical co-founder or senior dev on staff, at least one integration that Shopify's app store could not handle cleanly, and a visceral discomfort with paying a platform tax that grows proportionally with success. If that sounds like your situation, the migration is straightforward. If it does not, Shopify is probably still your best option -- and that is a perfectly fine answer.