Shopify B2B Wholesale Setup: A Complete Configuration Guide

Wholesale has changed, and Shopify finally caught up

A beauty brand we worked with last quarter was running their B2B channel through spreadsheets emailed to a sales rep, with draft orders manually built in the Shopify admin. They processed 340 wholesale orders a month. Two people. Forty-two hours a week on order entry alone. After moving to native Shopify B2B with self-service company accounts, the same volume took six hours a week. Not because wholesale got easier, but because the buyers placed their own orders through the portal.

TL;DR

▸ Shopify Plus ships native B2B with company accounts, price lists, and payment terms baked into one store ▸ Skip the old wholesale channel app; everything lives in the main admin now ▸ Model your B2B data as companies with locations and buyers, not as individual customer tags ▸ Self-service reorder is the retention lever; reps should handle onboarding and edge cases only

The B2B data model

The first thing to internalize is the three-level hierarchy.

Company. The legal entity you bill. "Acme Natural Foods LLC." Holds tax IDs, exemption certificates, and payment term defaults.

Location. Physical shipping addresses under the company. A single retailer might have 40 store locations. Each has its own address, catalog assignment, and payment terms override.

Customer. Individual buyers. One company can have many customers. Permissions control who places orders, who only views, and who approves.

Getting this model right at setup saves hours later. Treating every wholesale account as a customer with a tag works for five accounts, breaks at fifty, and is a nightmare at five hundred.

Catalogs and price lists

A catalog is a product set plus pricing rules assigned to specific company locations. You can run multiple catalogs simultaneously.

Default wholesale catalog. 50% off MSRP on every product. Assigned to all new companies.

Key account catalog. Tiered discount for high-volume accounts. Volume break at 12 units, better break at 48.

Exclusive SKU catalog. Products only available to certain distributor tiers. Common in supplements and outdoor categories.

Restricted catalog. Specific companies see only a subset of products, often to enforce regional exclusivity or brand channel rules.

The right number of catalogs is the smallest that covers your pricing policy. Three is common. Ten is complexity you'll regret.

Payment terms that actually work

Native payment terms cover net 0 (prepay), net 15, 30, 60, 90, custom fixed date, and custom number of days. Assign defaults at the company level.

Net 30 as default. Most wholesale accounts expect net 30. Setting this as the default payment term reduces checkout negotiation.

Credit limits. Shopify doesn't enforce credit limits natively. Bolt on Resolve, Balance, or Two for credit checks, limits, and AR offloading.

Prepay tier. New accounts start on prepay for the first 90 days. Graduates to net 30 after three clean orders. This is a policy choice, not a platform feature, but it's worth enforcing.

Purchase orders. Buyers enter a PO number at checkout that flows through to the order record and any connected ERP.

Onboarding workflow

How a new wholesale account gets set up is where most teams lose speed. The clean version:

Application form. Public-facing form capturing business name, tax ID, reseller certificate, estimated annual volume, and primary contact.

Review. Human approval step. Most teams rubber-stamp anyone with a valid reseller certificate and stated volume above a threshold.

Provisioning. Create the company, attach the reseller cert, assign the default catalog, assign payment terms, invite the primary buyer via email.

First-order handhold. Schedule a 20-minute call. Walk through the portal. Place the first order together. Answer questions.

Self-service from then on. Most accounts never need a rep again for routine reorders.

Our ecommerce strategy team sees the biggest wholesale wins come from compressing this onboarding from two weeks to two days.

Storefront configuration

B2B customers see the same storefront with B2B-specific behavior when logged in. The key configurations:

Catalog-gated pricing. B2B price replaces retail price when the buyer is authenticated and the catalog applies.

Quantity rules. Minimums, maximums, and increments per product. A case-pack of 12 means buyers purchase in multiples of 12. Enforce at the product level.

Quick order. SKU-search ordering for buyers who know what they want. Critical for repeat buyers; optional for new accounts.

Hide retail elements. Upsells, cross-sells, gift with purchase, and promo banners designed for DTC shoppers clutter the B2B experience. Template conditionals hide them for logged-in B2B buyers.

PDP simplification. B2B buyers don't need the same storytelling. Show price, stock, case-pack, and a reorder button.

Shipping, tax, and the headaches

Shipping. B2B shipping is usually freight, LTL, or customer-arranged carriers. Configure shipping profiles that route B2B orders to flat-rate freight, quote-on-request, or customer pickup.

Tax. Reseller certificates override sales tax at checkout. Upload per company location for multi-state coverage. Our compliance audit team finds this is where most B2B channels leak money; either over-collecting tax on exempt buyers or under-collecting on non-exempt states.

Duties. For international B2B, DDP vs DAP decisions matter more than in DTC. Net-term buyers want predictability. Quote DDP whenever possible.

The SNAP framework for B2B readiness

Before launching, run every dimension through SNAP.

S — Setup. Company, location, customer hierarchy built. Catalogs assigned. Payment terms configured. Resale certs uploaded.

N — Navigation. Logged-in storefront works. B2B price displays. Quantity rules enforced. Retail clutter hidden.

A — Automation. Order routing to ERP/3PL. Payment terms collection. Invoice email triggers. Reorder workflows.

P — People. Sales rep handoff defined. Customer service trained on B2B vs DTC differences. AR process for net terms.

If any pillar is shaky, ship anyway with manual workarounds and fix within 60 days. Waiting for perfection kills most wholesale launches.

Comparison: native B2B vs wholesale apps vs second store

For most Plus merchants, native B2B is the answer. We break down the trade-offs more in our wholesale channel launch guide.

Integration with retention and service

B2B retention is fundamentally different from DTC. The lever is reorder frequency, not list size.

Email flows. Net terms due reminders. Reorder prompts at typical buying intervals. Restock alerts on hero SKUs. Our retention marketing service rebuilds these flows for every B2B launch.

Customer service. B2B tickets are higher stakes and often involve larger orders. Route to a dedicated queue with senior reps. Our customer experience service details the org structure.

Account management. Assign a rep to any account doing meaningful monthly volume. Quarterly check-ins, new product previews, promotional planning.

Reporting and what to watch

B2B metrics diverge from DTC. The numbers that matter:

▸ Active accounts (ordered in last 90 days) ▸ Reorder rate by cohort ▸ AOV by account tier ▸ Days sales outstanding on net terms ▸ Catalog coverage (% of products ordered per account) ▸ Self-service rate (% of orders placed without rep assistance)

Build dashboards for these specifically. DTC dashboards don't translate.

What breaks when you add B2B to an existing DTC store

Promotion logic. DTC discount codes may stack incorrectly with B2B catalog prices. Audit every active promotion before launch.

Inventory. Wholesale orders drain inventory fast. A single wholesale order can equal 200 DTC orders. If your DTC engine assumed steady drain, buying plans need updating.

Accounting. DTC revenue and B2B revenue should hit different GL accounts. Wire this into your ERP sync before the first invoice.

Fulfillment. Most 3PLs handle DTC and B2B on separate workflows. Coordinate before you send a 40-case pallet to a DTC-only warehouse.

Related reading

For brands deciding whether to spin up wholesale alongside DTC, the wholesale channel launch playbook covers the commercial math. Our Faire vs NuORDER comparison (platform overview) helps with marketplace decisions. The 3PL transition playbook matters if your current 3PL can't handle wholesale.

What to do this week

▸ Confirm Shopify Plus access and enable the B2B features in your plan ▸ Draft the company/location/customer data model for your top five target accounts ▸ Define your default wholesale catalog and one tiered volume catalog ▸ Write the application form and onboarding SOP ▸ Audit active DTC promotions for B2B catalog conflicts before you flip anything on

Native B2B is the biggest unlock Shopify has shipped for DTC brands with real trade demand. Don't keep running it on spreadsheets.