The Complete Guide to Automating B2B Orders in Shopify

Introduction

Running a B2B or wholesale store on Shopify often comes with special challenges: customers send purchase orders by email, pricing varies per customer or company, and buyers rarely use the DTC-style checkout flow. Many merchants still manually retype purchase orders into Shopify — costing hours of work and creating avoidable errors.

The good news? Shopify now provides powerful B2B features, and with the right automation workflow, you can process email or PDF orders instantly without typing a single line item.

This guide explains how to properly set up Shopify for B2B, and then how to automate incoming PDF/email orders into draft orders.

1. Before You Automate: Set Up Shopify Properly for B2B

Most automation fails because the Shopify B2B foundations are not configured correctly.
Here’s what every wholesale merchant needs:

1.1 Set up the customer or company (Shopify Plus)

Shopify B2B works differently depending on your plan:

If you’re not on Shopify Plus:

• You’ll add customers normally in “Customers.”

• You can group them using tags (e.g., “wholesale”, “distributor”, “VIP”).

If you’re on Shopify Plus:

You get access to Companies, which allow:

• Multiple locations under one company

• Location-specific price lists

• Payment terms

• Tax overrides

• Customer associations with one or more companies

For B2B automation, this matters because the draft order needs to link to the correct:

• Customer

• Company

• Company location

• Price list

If the buyer isn’t set up correctly, the draft order will not reflect the right B2B price or payment terms.

1.2 Set up B2B pricing (customer or company price lists)

Your automation can only apply the right wholesale price if Shopify knows what that price is.

Options:

Standard Shopify (non-Plus)

• Use discounts, compare-at prices, or automatic discounts

• Use customer tags to activate a discount rule

• Use apps that maintain customer-specific price lists

Shopify Plus B2B

You should absolutely create:

• Price lists

• Customer-specific or company-specific pricing

• Volume tiers (optional)

Why this matters for automation:
When the system creates a draft order from a PDF/email, Shopify automatically applies the correct:

• Price list

• Discounts

• Payment terms

…but only if they’re configured properly.

1.3 Ensure every product has a SKU and a clear description

This part is critical.

Automation tools rely on:

• SKU

• Product name

• Variant title

• Sometimes handle or GTIN

If your PDF purchase orders contain “SKU 12345” but your product is missing that SKU in Shopify, the system will struggle to match items.

Checklist:

✔️ Every product and variant has a unique SKU
✔️ Product titles are clean, consistent, and descriptive
✔️ Variant titles follow a consistent format
✔️ No duplicate SKUs (very important)
✔️ Add keywords your B2B buyers use in descriptions

A clean catalog = clean automation.

2. B2B Orders Don’t Fit Shopify by Default — Why

Most B2B buyers:

• Prefer sending purchase orders by email

• Use their ERP or accounting system

• Want negotiated pricing

• Don’t use the Shopify checkout

• Need payment terms (“net 30”, etc.)

This is why Shopify merchants end up manually creating draft orders — and why automation is so valuable.

3. The 3 B2B Workflows You Can Automate Right Now

3.1 Automatically convert PDF or email POs → Shopify draft orders

This is the biggest time-saver.

Automation tools like LevelOps PDF-to-Order extract:

• SKUs

• Product names

• Quantities

• Customer identity

• Notes or delivery instructions

And then create a Shopify draft order linked to:

• The correct customer

• Or the correct company + location (Shopify Plus)

• The correct price list

• Payment terms

A process that takes 5–10 minutes manually becomes automatic.

3.2 Automatic order confirmations

After a draft order is created, the system can send:

• A confirmation email

• A notification to your staff

• A Slack alert

• Or all of the above

This dramatically improves customer response time.

3.3 Alerts for errors or unmatched items

If a PDF includes:

• A wrong SKU

• A discontinued product

• A format Shopify doesn’t understand

You get an instant alert so you can fix it before fulfillment.

No more hidden mistakes.

4. Benefits of B2B Automation on Shopify

• Zero manual typing

• Consistent, accurate order creation

• Faster PO turnaround

• Proper pricing & payment terms applied every time

• Fewer staff resources needed for data entry

• Happier wholesale customers

• Scalable even with high-volume purchase orders

5. Conclusion

Shopify can be a powerful B2B platform — but only if stores configure customer/company setup, pricing, and product data correctly. Once these foundations are in place, automating PDF/email purchase orders becomes effortless.

For wholesale and manufacturing businesses, order automation isn’t just a convenience — it’s a competitive advantage that saves hours of work every week and eliminates costly errors.