Native Shopify B2B vs Wholesale Apps: Which Setup You Actually Need

You have trade customers. Maybe a dozen stockists ordering by email and a spreadsheet, maybe a hundred accounts with their own price lists and 30-day terms. Either way the question is the same: do you run wholesale on Shopify native B2B, bolt on a wholesale app, or spin up a separate store? If you have read our explainer on what Shopify B2B and wholesale actually involves, this is the decision that follows it.

The honest answer changed in 2026, and most of the advice still online has not caught up. Here is where the three options stand now, and how to choose between them without paying for infrastructure you do not need.

Native Shopify B2B: no longer Plus-only

Until spring this year, native B2B was a Shopify Plus feature, full stop. On 2 April 2026 Shopify moved most of it to Basic, Grow and Advanced at no extra cost. On any plan you now get B2B company accounts with multiple locations and buyers, catalogues that set trade pricing and product availability, net payment terms, vaulted cards, quantity rules (minimums, maximums and case increments), volume pricing, quick ordering and a B2B checkout that understands all of it. Shopify Flow can automate approvals and tagging around the lot.

What stays behind the Plus wall is narrower than it used to be, but it matters:

Catalogue count. Basic, Grow and Advanced are capped at three active B2B catalogues across all your B2B markets. Plus is unlimited.Direct assignment. On lower plans a catalogue attaches to a B2B market, so every company in that market sees the same prices. Only Plus lets you assign a catalogue to a specific company or location, which is what account-level pricing really means.Deposits and partial payments. Taking a deposit at order and the balance at fulfilment is Plus only, as are per-fulfilment payment requests.Scale. Plus bundles nine expansion stores, deeper checkout customisation and the operational tooling you need once trade is a serious channel.

The catalogue cap and the market-level assignment are the two that bite. Three catalogues covers retail, trade and key accounts, and nothing more. If buyer A pays 40% off and buyer B pays 45% off with a different minimum, you will run out of catalogues fast, or you will be bending your Markets structure out of shape to fake it. Note too that catalogues on the lower plans require the new Shopify Markets, so older stores may have a migration step first.

App-based wholesale on Shopify: cheaper, more flexible, more fragile

Before April, the app route was how almost everyone ran a wholesale Shopify setup without Plus. The pattern: tag approved customers, show them discounted pricing through an app or automatic discounts, gate wholesale collections behind login, add a bulk order form, and handle terms with draft orders or an invoicing app. Some brands go further and run a password-protected wholesale storefront fed from the same catalogue.

It works, and at £20 to £60 a month in app fees it is hard to argue with for a handful of accounts. Tag-based apps also do things native B2B still does not: per-customer pricing that is truly individual on a lower plan, cart-level volume tiers that look at the whole order rather than one product, and registration forms with approval flows that feel finished.

Where it creaks:

Discounts are a workaround. Trade prices are usually discounts layered on retail prices. They collide with promotions, with Shopify discount combination rules and with any other app that touches the cart.Checkout is the retail checkout. No terms, no PO numbers without customisation, no real company structure. A buyer with three branches is three customer records.Reporting is messy. Wholesale and retail revenue blend together in Shopify Analytics unless you tag everything perfectly, forever.Every app is a dependency. Theme updates, checkout changes and the app vendor's own roadmap can all break a flow your trade customers rely on.

Mixing native catalogues with app discounts for the same buyer is where we see the worst outcomes. Pick one pricing engine and let it own the number.

The separate store option

The third route is a dedicated B2B store: its own domain, theme, catalogue and checkout, either as a Plus expansion store or a second standalone plan. It is the cleanest separation and the heaviest to run. Two themes to maintain, two sets of apps, two inventories to keep aligned (or an ERP in the middle), and two places to fix when something breaks.

It is justified when the trade proposition is genuinely different: a different range, pack sizes rather than units, prices that must never be visible to the public, trade-only content, or a legal reason to keep channels apart. If 80% of the catalogue overlaps and the only difference is price, a blended store with native B2B is simpler and usually converts better, because you keep one set of product pages that you have already put the conversion work into.

The decision factors, plainly

Work through these in order. The answer usually falls out by the fourth.

Number of trade accounts. Under about 20 active accounts on similar terms: native B2B on your current plan, or an app if you already run one happily. Dozens of accounts with individual deals: you need direct assignment, which means Plus or a very disciplined app setup.Pricing complexity. One or two trade tiers fit in three catalogues. Account-specific price lists, negotiated SKUs or regional trade pricing do not.Self-serve versus rep-led. Gartner's latest sales survey, published March 2026, found 67% of B2B buyers prefer a rep-free experience. If your buyers reorder themselves, a proper B2B checkout with saved terms and quick order pays off quickly. If a rep keys every order, draft orders and a spreadsheet are not the embarrassment people think they are.ERP and finance. Credit limits, terms enforcement and invoicing usually live in the ERP, not in Shopify. Check what your integration supports before you choose, because the wrong setup here creates manual work every single day.Payment terms and credit. Native net terms work on every plan now. Deposits and staged payments are Plus only.Catalogue overlap. High overlap favours a blended store. Low overlap favours a dedicated one.

Be honest about the Plus jump

Shopify Plus starts at around £1,800 a month in the UK on a three-year term, more on shorter terms, before apps, theme work and the time it takes to actually use what you are paying for. Advanced is £344 a month. That gap buys unlimited catalogues, direct assignment, deposits, deeper checkout customisation, expansion stores and higher API limits. It does not buy a single extra trade order.

B2B alone should rarely be the reason to upgrade. It should be one line in a wider case that includes retail volume, international expansion, checkout customisation and operations. We have written about when Plus is actually worth it, and the summary is the same here: if the only thing forcing the move is a fourth catalogue, you are paying roughly £17,000 a year to avoid a process conversation.

For plenty of brands with a handful of trade accounts, an app and a good process is the right answer for another year. The job is to notice when that stops being true.

What we would do

If you are on Basic, Grow or Advanced with trade customers and no B2B setup, turn on native B2B first. It is included, it is maintained by Shopify, and three catalogues cover most brands at this stage. Move an existing tag-based wholesale setup across only when you can retire the app cleanly. Running both in parallel is the one thing we would not do.

If you are hitting the catalogue cap or buyers need genuinely individual pricing, cost Plus as a whole-business decision, not a B2B one. And whichever route you take, remember the trade storefront is a conversion surface like any other. Most Shopify brands do not have a traffic problem, they have a conversion problem, and a wholesale buyer who cannot find pack sizes or reorder in two clicks is revenue you already paid to acquire.

We are a senior Shopify team based in Glasgow, working with brands across Scotland, the UK and further afield, and B2B setup decisions come up in most of our Conversion Growth Retainer engagements. If you want a second opinion on native versus app versus separate store for your account list, get in touch and we will give you a straight answer, including when the answer is to stay exactly where you are.