Shopify agencies aren’t ERP experts
Stop letting them tell you otherwise
The following article is self-serving, given the business models of Commerce Thinking and HighCohesion, but that doesn’t make it any less true.
I keep seeing the same moment in Shopify agency decks. The slide where they tell the room “we’re experts in ERP”.
It’s the throwaway line in every deck, and so common that many brands don’t always stop to question or scrutinise it.
Then the same brands are 3-6 months into a new site build or migration project. And the flow of data in and out of the ERP is being rejected by Finance because the numbers don’t line up.
Or worse, the gaps in data or the errors in setup aren’t detected until post go-live.
Then it goes wrong and month-end takes longer, reconciliation throws up surprises, and confidence in the system evaporates across finance, ops and merch.
That’s the moment that should make you sweat. Not because ERP is scary, but because a lot of agencies aren’t actually selling ERP expertise.
They’re selling familiarity with connecting to ERPs. They just don’t truly realise it (or do, and are pulling the wool).
ERP integration isn’t ERP expertise
No one’s the bad guy here (unless you’re knowingly pulling the wool, if so, get f****d). The market’s packed with teams who can build slick storefronts, amazing site back ends, and chase conversion, and it’s still harder to find people who can talk about Shopify like an ops system that has to reconcile cleanly into finance.
The problem is what happens next. That shallow exposure gets mistaken for knowing what good looks like, and then somebody confidently starts making decisions that belong in finance, ops, and systems.
If you’re a brand-side operator reading this, you know the situation. The people least qualified to decide how orders should land in the ERP are often the people talking the most in the meeting.
If you’re an agency reading this, you’ve probably felt it too. Your team can build the storefront, then the conversation drifts into transaction types in ERP, allocation logic, partial shipments, and returns. And suddenly you’re out of your depth, live, in front of the client.
Quick test. Can your ERP operator walk a real order end to end without sweating under questioning from finance? How an order type shows up in the chart of accounts? How to update payments? How to map out all the related records? How to configure ERP connections to 3PL to handle inventory adjustments linked to returns?
If not, you’ve got a connector. Not an ERP specialist.
I know because I used to think I was an ERP specialist, until I worked with Dom and Maxime on the Commerce Thinking team and realised “oh shit, that’s what being an expert in this really means”.
What shallow ERP integration looks like
A lot of agency-led ERP work looks like this. Orders go from Shopify into the ERP, inventory comes back, and someone declares it job done.
That’s a start. But it’s also not the hard part.
The hard part is everything that sits around those syncs. Exceptions, data ownership, and who fixes what are the boring bits that decide whether the system behaves at scale.
The ugly truth is the integration often doesn’t fail loudly. It just quietly does the wrong thing, or never does the thing you assumed it was doing.
We’ve seen this play out. An integration between multiple Shopify expansion stores into a multi-subsidiary NetSuite instance that had been hobbling along for 12 months with gaps in data, low trust in the accuracy of sales and refunds data in NetSuite, all after a stressful 9 month migration project led by the Shopify agency. And Commerce Thinking are able to square the issues away in <12 weeks.
Who pays when you over-claim
First, your client pays.
When the ERP and webstore don’t work together cleanly for departments like Finance, Ops, Merch, then the cost shows up everywhere. Orders get retyped and inventory drifts, and finance ends up having to reconcile the long way and never really trust their numbers. Merch start to rely on data exports from other systems and portals because they don’t trust the numbers in ERP either.
Second, you pay.
These projects stop being profitable for a generalist agency the moment they go sideways. You either eat the hours, or you go back for change requests and watch trust drain away.
Then your reputation takes a quiet hit. The client stops treating you like the grown-up in the room.
They might not fire you immediately. They just stop inviting your ERP lead to the important calls, because they’ve clocked you’re not helping.
If you’ve ever wondered why you got dropped from the integration workstream but kept on the site tweaks, that’s what happened.
Why this keeps happening
Part of this is structural. Shopify’s partner ecosystem is brilliant at front end, design, dev, and growth, and it’s thin on back-office operators.
So agencies stretch. Clients assume it’s normal. Everyone walks into the room with the wrong expectations.
The agencies also want to control as many dependencies inside a project and capture as much of the clients wallet as possible. Adding integration to their service lines makes sense through that prism. But ignores the fact they’re not qualified.
The other part is risk and complexity. Integration projects like this have a habit of running late, overrunning, and breaking in ways that only show up once you’re live.
If you’re treating that risk as a bolt-on service line, you’re gambling with your client’s operation and your own credibility. So you better be fucking good.
The better move for agencies
Don’t pretend you’ve got ERP covered. Be the agency that knows exactly where your expertise ends, and brings in the right people before the client loses confidence.
Drop the act. Not because you’re bad at your job, but because you’re playing a game you can’t win.
If you want a practical way to run this, keep it boring.
Own the scope. Lead Shopify, UX, and front end delivery, but don’t let yourself get cast as the person designing finance and ops workflows.
Bring the specialist in early. Discovery, data mapping, and end-to-end testing are where projects are won or lost, not when everyone’s stressed and trying to save face.
Price and plan for the initial period after go-live. That’s where the ugly stuff shows up, and where most teams get found out.
None of that makes you smaller. It means you do less, better, more profitably.
It also makes you look better to the client, because you’re not forcing them to put up with you learning on the job.
Where Commerce Thinking fits in
This is the bit where we stop dancing around it.
This is why Commerce Thinking exists. Our work sits in the unsexy middle where Shopify touches finance, ops, and ERP, and we tend to get pulled in when someone wants it owned properly.
If you’re an agency owner and you want to keep the client relationship and still get these projects delivered cleanly, bring us in early. Not to take your client, but to make sure the bits that can make you look naive don’t become the lasting impression.
If you’re a brand-side operator and your agency is leading ERP conversations, push a bit. Ask who owns end-to-end testing, who owns reconciliation, and who owns the initial period after go-live.
If you’re not convinced by the answers, or want some help qualifying the answers just get in touch. Our ERP study programme is designed for brands in your position. Let us take a look under the lid and help you to do a migration properly from the start, rather than a rescue job later.
If this hit a nerve, get in touch. We’d rather have the awkward conversation now than watch you have it with your client later.