Hey everyone. I own a business that has been operating on a Squarspace site for 8+ years and we’re looking to FINALLY transition over to a Shopify store. We built our store in a time where direct integrations into stripe were common place and in the 8 years since, we’ve only deepened our dependence on Stripe building out custom workflows and internal tools for processing invoices for our resellers and B2B customers. Literally our entire business operates around our Stripe account.
We’re a team of 7 people now based in the US with 2 full time developers doing about $1m in revenue through our direct to consumer online store processing about 20k transactions per year. I really want to transition to Shopify for our DTC as it makes a lot of the backend work much easier, however, I am NOT okay transitioning to Shopify payments.
Yes, I totally understand Shopify payments IS Stripe, but it’s a Stripe we don’t fundamentally control. From the looks of it, a lot of the underlying API’s are exposed in shopify payments but there are plenty that look like they are blocked or just not stated if they are supported. (Or so I am told from my developers)
I’ve reached out to Shopify support and was subsequently escalated two levels explaining that we do not wish to use Shopify payments due to our own custom tooling. Each step along the way, they tried to convince us to use Shopify payments but we respectfully declined. Eventually after a few days, we were told that they would not provide any exception but no reason why. The first two support agents even agreed we likely qualified for an exception based on our history alone but they were not able to make the decision and that a manual review was needed.
Is there something I am doing wrong here? Is this just that Shopify is locking down their platform making it more difficult to use third party gateways outside of their walled garden? Do I have any hope of bringing my own Stripe account along for the transition?
At the end of the day, I am sure we could make Shopify payments work, but out of principle now I really don’t want to as this seems so heavy handed to force this on businesses with established relationships. Ive paused my developers and I’ve canceled our advance plan for the time being. I get that I’m likely small potatoes to some of the customers here, I would just like it to make sense.
Fair concern and the answer depends on whether you go standard or Plus. Shopify Payments is Stripe under the hood but the account isn’t yours. You don’t get the Stripe dashboard, can’t pull payment_intent IDs out the front door, and webhooks come from Shopify not Stripe. For your existing B2B and reseller tooling that matters a lot.
Three real paths worth considering:
Keep Shopify DTC on Shopify Payments, keep B2B and resellers on your current Stripe account. They don’t need to share a processor. You lose some reporting unification but your custom tools stay put. Cleanest if your B2B flow isn’t going through the Shopify checkout anyway.
Use a third-party payment gateway at checkout (Stripe available outside the US on some plans, or via Authorize.net relay). Shopify charges a 2% transaction fee on non-SP gateways on standard plans, 0.15% on Plus. At $1M that’s $20k/year on standard vs $1.5k on Plus. Plus also gives checkout.liquid and checkout extensibility which makes passing metadata back to your Stripe flow survivable.
Shopify Plus with Stripe Connect style setup through a partner. Some agencies build this but you’re deep in custom-dev territory and you’re still processing through Shopify’s instance.
The hidden cost nobody mentions: even on Plus the checkout emits Shopify order webhooks, not Stripe payment webhooks. If your reseller tooling keys off Stripe events directly you’ll need a translation layer.
Are you thinking standard or Plus? That answer shifts the math significantly.
We initially signed up for the advanced plan for the development transition, but we were totally onboard moving over to plus because we did do that math and it made sense to at our revenue levels. We just wanted to make sure we could do what we wanted how we wanted to before jumping all in. We also tried explaining this to the support agents and I believe their tier 2 (third person I talked to) was super understanding and mentioned they would note this in our account and forward this onto the review team. Not sure if that helped us or hurt us… Standing to make $20k on extra fees, or something like $27k on a platform revenue and passing on that is just odd but I guess it’s their walled garden.
We’re not opposed to some custom development work, even some pretty gritty stuff, but it has to make sense of course. Before this interaction we thought it would have been far simpler to just run with it. Guess we didn’t know what we didn’t know.
We are looking into third party gateways and I agree on your point that our B2B and DTC do not have to share the same processor. It’s super nice not going to lie, but not the end of the world either. We have customers that eventually turn into B2B customers so being able to have workflows that make that easy is something that was appealing. We thought by moving over to Shopify this was actually going to make this even easier since it would allow us to implement custom user pricing, MOQ, terms etc instead of having to use our own internal tooling as much.
At the end of the day, we will make something work… Just sad to see a platform that claims to offer so much set up these esoteric roadblocks.
On Plus you actually have most of this natively without touching Stripe Connect. Shopify B2B is the piece that’s easy to miss in the docs.
Graduation flow: same customer record across DTC and B2B contexts. You tag the customer or attach them to a Company, they see DTC pricing or catalog pricing depending on which storefront. Shopify Flow handles the auto-tag on LTV or order count thresholds.
Custom pricing, MOQ, net terms: catalogs and price lists are per-Company. MOQ at variant level, net 15/30/60 with no upfront card, quantity rules per buyer. That’s the part your current setup can’t replicate without your B2B tooling.
The friction you’ll still feel is the existing Stripe-based reseller workflows already onboarded. Two paths: rebuild on B2B’s payment-terms logic and reconcile via order webhooks, or keep those accounts on your standalone Stripe off-platform and migrate slowly. Rebuild is less work than it sounds because B2B already encodes Companies, locations, and assigned buyers, which is most of what custom tooling typically wraps.
Anything that genuinely needs Stripe-direct (metered, mid-cycle adjustments) is checkout extensions on Plus, no Connect needed.
You’re not doing anything wrong, Shopify just won’t allow external gateways in native checkout, no matter your history.
If keeping full control of your Stripe account is non-negotiable, your only real option is using a custom Stripe-based checkout integration. That way you keep your existing workflows, APIs, and B2B logic intact.
If you don’t want unnecessary headaches, you should either build something tailored to your own needs or use services that already offer this out of the box. Stripe and its capabilities are powerful, but you only get full control over them through more advanced, tailored setups.
The hard part with this kind of migration is usually not the payment method itself, it’s preserving the reseller / B2B logic around it.
If buyers are already used to ordering on terms, I’d map the flow around Companies, payment terms, and outstanding exposure first, then decide how much needs to stay in Stripe versus Shopify.
The risk is rebuilding the payment path but leaving finance with the same manual review problem.
For B2B, I’d want a rule at checkout that knows whether the company is still within its approved limit before the order is accepted.