In today’s digital commerce landscape, business-to-business (B2B) eCommerce is no longer a nice-to-have — it’s essential. If you’re running a wholesale business, distributor or supplier, building your B2B channel on a platform like Shopify can unlock major growth. At WaffleBytes, we’ve seen how the right setup can increase order value, streamline operations and deliver a professional buying experience for your business customers.
In this guide we’ll walk you through how to set up B2B eCommerce on Shopify — from choosing the right store structure to configuring catalogs, pricing, payment terms, shipping rules and integrations with backend systems. Whether you’re purely B2B or you combine B2B + D2C (direct-to-consumer) in one store, you’ll find actionable steps and best practices.
1. Choosing the Right Shopify Store Type
Before you dive into the technical setup, you need to decide how your B2B sales will be structured on Shopify. According to Shopify’s own documentation, B2B features are only available on the Shopify Plus plan. Shopify Help Center+2Shopify Help Center+2
Here are your two main options:
Dedicated B2B Store: A separate Shopify store solely for business customers. Offers clean separation of catalogue, pricing, inventory, and operations. Shopify Help Center+1
Blended Store (B2B + D2C in one store): You maintain a single store serving both business and retail customers, using B2B features to segment business buyers. Shopify Help Center+1
Choosing between them depends on how big your wholesale business is, whether you share stock between B2B and D2C, and operational complexity. At WaffleBytes we advise: if your B2B orders are high-volume or you need isolated inventory/pools, go dedicated. Otherwise, a blended model keeps things simpler.
2. Upgrade to Shopify Plus & Enable B2B Features
Because many B2B functionalities are only included on Shopify Plus, your first step is to upgrade (if you haven’t already). Webiators+1
Once you’re on Plus:
In Shopify Admin go to Settings → B2B to enable the features. Webiators
Decide on whether you’ll invite business customers (clients must log in) or open registration (businesses sign up).
Create internal workflows for approving B2B accounts before granting access to business-specific catalog and pricing.
3. Set Up Companies and Customer Accounts
One of the key differentiators of B2B on Shopify: you’re selling to companies, not just individuals. Shopify allows you to set up Companies with multiple Company Locations, mapped to customers. Shopify Help Center+1
Steps:
In Shopify Admin, go to Customers → Companies, create the company record.
Add multiple locations (shipping addresses, billing addresses) under the company.
Assign customers (login‐accounts) to those companies / locations.
Configure company-specific attributes: payment terms (Net 30, Net 60), tax exemptions, special shipping addresses. Shopify Help Center+1
Optional: import existing customer / order history data with tools such as Matrixify or CSV. Shopify Help Center
By doing this, your business buyers will view their own portal with tailored pricing, checkout terms, shipping rules and order history — a true self-service wholesale experience.
4. Create Custom Catalogs & Price Lists
In B2B you rarely sell the same price to everyone. Shopify’s B2B features allow you to create catalogs (product sets) and assign them to specific companies or locations. Shopify Help Center+1
Implementation steps:
Define different product catalogs: e.g., “Wholesale USA”, “Distributor Canada”, “Large Volume Europe”.
Assign products and pricing tiers to each catalog.
Configure quantity rules: minimums, increments, pack sizing. Third-party apps such as SparkLayer can help if Shopify’s native tools are not sufficient. SparkLayer B2B eCommerce
Link catalogs to companies via their assigned location, or via markets if you sell internationally.
Hide certain products from B2C or hide B2B-only products from retail visitors (in a blended store scenario). Shopify Help Center+1
Tip for WaffleBytes clients: Make sure your product SKUs, naming conventions and inventory strategies are aligned with wholesale logic (e.g., bulk packs, box deals, plus volume discount tiers).
5. Configure Payment Terms & Shipping Options
Wholesale often involves terms like “Net 30”, “Invoice”, “Purchase Order (PO) number”, and custom shipping logistics. Shopify B2B supports these features. Shopify Help Center+1
Payment & Checkout:
Set manual payment methods (bank transfer, check, credit account) for B2B companies.
Use Shopify Flow to automate triggers: e.g., when payment is due, send reminders; when PO is linked, convert draft order to invoice. Shopify Help Center
Require PO number on checkout or draft-order form.
Enable partial payments, deposits, or credit limits if you have them.
Shipping & Fulfilment:
Create shipping profiles for B2B: e.g., freight shipping, large-parcel carriers, LTL.
You can hide certain shipping methods for B2C customers but make them available for B2B via “Checkout Blocks” or conditionals. Shopify Help Center
Set delivery rules by company location (e.g., multiple ship-to addresses for a buyer).
6. Theme Customization & User Experience Optimisation
Your buyer’s experience should feel like a professional B2B portal. Shopify provides themes and features built for wholesale. PageFly+1
Key UX Elements:
Use a wholesale-focused theme (Shopify’s “Trade” theme is an example). PageFly
Require B2B customers to log in before seeing pricing/catalogs (for blended store setups).
Offer quick-order forms (bulk add SKUs, CSV upload, reorder past orders).
Provide account portal: past orders, invoices, order tracker, reorder functionality.
Customize content banners, messages to B2B vs B2C visitors.
Tip: Tailor the theme to display “Net 30 terms”, “Request quote”, or custom banners like “Welcome, [CompanyName]”. This builds trust and professionalism.
7. Integrate with Back-Office Systems & Automations
B2B operations often involve ERP, CRM, DMS, accounting and fulfilment systems. To scale, integration is key. Shopify provides APIs and apps to support this. Shopify+1
Areas to integrate:
Inventory & stock levels (especially if sharing between B2C and B2B).
Order management (draft orders for B2B, PO workflows).
Accounting / invoicing (push order into accounting system).
Customer data (CRM with company structure).
Tax & compliance (e.g., tax exemption for business customers).
At WaffleBytes, we always recommend mapping your data flows early: how will a B2B order update your inventory? How will a payment-term invoice sync to accounting?
8. Testing, Launching & Operating Your B2B Channel
Before you go live, thorough testing and operating readiness are essential.
Pre-Launch Checklist
Create a test company and test customer account in Shopify. Shopify Help Center
Place sample orders in B2B mode: test custom pricing, terms, shipping, multiple locations.
Verify that D2C customers (if blended store) cannot see B2B-only products or pricing.
Ensure checkout terms/P.O. number fields are working, payment methods toggle correctly.
Validate analytics & reporting: B2B orders might behave differently (larger order value, different tax/shipping).
Post-Launch Operations
Monitor initial orders, feedback from business customers.
Fine-tune user account onboarding for companies (approval process).
Use automation (Shopify Flow, or apps) for tagging, notifications, approvals.
Regularly review catalog pricing, volume discounts, and seasonal promotions for business buyers.
9. Common Challenges & How to Address Them
Stock pool conflicts: If B2C and B2B share the same inventory, one group may deplete stock. Solution: segment inventory or use a dedicated store. SparkLayer B2B eCommerce
Pricing complexity: Wholesale businesses often need tiered volume pricing, special discounts, or negotiated pricing. If Shopify out-of-the-box isn’t enough, consider a third-party app like SparkLayer. SparkLayer B2B eCommerce+1
User experience for business buyers: Some businesses expect advanced features (bulk upload CSV, PO numbers, account statements). Without them it may feel less “enterprise”.
Integration gaps: Lack of back-office integration (ERP, CRM) can cause operational strain. Plan your systems ahead.
Onboarding & access control: Business accounts must be approved, and pricing hidden unless logged-in to avoid retail discounting errors.
10. Why Choose WaffleBytes to Implement Your Shopify B2B Channel?
At WaffleBytes, we specialize in helping wholesale brands and distributors launch and scale B2B eCommerce on Shopify. Our key advantages:
Full understanding of the unique requirements of B2B: company hierarchies, catalogs, payment terms, quoting workflows.
Proven methodologies for both dedicated B2B stores and blended B2B + D2C models.
Integration-first approach: ensuring inventory, orders, accounting and CRM are connected.
UX-driven design: user experience for business buyers that drives larger orders and repeat purchases.
Post-launch support: training, automation and monitoring so you’re not left on your own.
If you’re ready to transform your wholesale business with Shopify and get it running smoothly for business customers, contact WaffleBytes and let’s talk about your roadmap.
Yes. Many of Shopify’s native B2B features (companies, catalogs, business pricing) require the Shopify Plus plan.
Yes — that’s called a blended store. You’ll use features like customer segmentation, catalog assignments and hidden pricing to serve both types of customers from one store.
Use Shopify’s catalog and pricing features to assign product sets and prices to specific companies or company locations. For more advanced rules (tiered pricing, whole customer-specific discounts) you may need third-party apps like SparkLayer.
While not mandatory, integration is highly recommended. It helps sync inventory, pricing, order fulfilment and accounting, which are critical for wholesale operations.
First, set up the company account structure in Shopify. Then provide a registration or invitation form for business customers. Use an approval workflow so that only verified businesses get access to wholesale pricing and approvals. Make sure the user experience is smooth and the login/account area is clear and professional.
Setting up a B2B eCommerce channel on Shopify is more than just flipping a switch—it’s about designing an experience tailored for business buyers, with pricing, catalogs, payment terms, shipping rules and integrations that speak their language. With the right approach, your wholesale business can scale online, win larger orders, and become a trusted supplier to other businesses.
At WaffleBytes, we help brands like yours build, launch and optimise Shopify-based B2B stores that deliver real results. If you’re ready to take your wholesale eCommerce to the next level, we’d love to partner with you.
