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.
Most automation fails because the Shopify B2B foundations are not configured correctly.
Here’s what every wholesale merchant needs:
Shopify B2B works differently depending on your plan:
You’ll add customers normally in “Customers.”
You can group them using tags (e.g., “wholesale”, “distributor”, “VIP”).
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.
Your automation can only apply the right wholesale price if Shopify knows what that price is.
Options:
Use discounts, compare-at prices, or automatic discounts
Use customer tags to activate a discount rule
Use apps that maintain customer-specific price lists
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.
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.
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.
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.
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.
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.
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
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.