Shopify B2B Orders Through a 3PL: Wholesale Without a Second System

Written By

Hafez Ramlan

Last Updated:

Warehouse worker moving stacked cartons with a pallet jack between metal shelving

Short answer: Since April 2026, Shopify's native B2B features (company profiles, up to three custom catalogs, quantity rules, vaulted cards and payment terms) are available on the Basic, Grow and Advanced plans, not only on Plus. Shopify B2B orders land in the same order list as your direct-to-consumer orders, so a 3PL that imports your Shopify orders can usually fulfill wholesale without a second system. The real work is making sure the warehouse can tell a B2B order apart and ships it to wholesale standards: case quantities, the buyer's PO number, the right ship-to location, and parcel or pallet depending on size.

What changed with Shopify B2B in 2026?

Shopify announced on April 2, 2026 that core B2B tools were coming to all plans at no extra cost. According to Shopify's announcement:

Now on Basic, Grow and Advanced: company profiles for wholesale buyers, up to three custom catalogs with tailored pricing, volume discounts and quantity rules, vaulted credit cards, and payment terms.
Still Plus-only: unlimited catalogs, direct catalog assignment to companies and locations, partial payments and deposits.

For many brands that were running wholesale through a separate portal, spreadsheet or app, this means wholesale buyers can now order in the same Shopify store as consumers. That is good for a 3PL relationship, because one integration carries both order streams.

How is a B2B order different from a DTC order in the warehouse?

Detail	Typical DTC order	Typical Shopify B2B order
Quantity	1 to 3 units	Cases or inner packs, often dozens of units
Ship-to	A home address	A company location with receiving hours
Paperwork	Branded packing slip or none	PO number on the slip and carton labels; often no retail prices
Packaging	Mailer or branded box	Master cartons, sometimes palletized
Carrier	Parcel	Multi-carton parcel or LTL freight
Timing	Ship today	Ship by a requested date, sometimes not before one

None of this is exotic for a 3PL that already does wholesale. The risk is that a B2B order slips into the DTC flow and ships as 48 loose units in a mailer with a consumer packing slip.

How do you set up the Shopify B2B to 3PL handoff?

Make B2B orders identifiable. Agree on how the 3PL recognizes them, such as an order tag, the company name on the order, or a separate sales channel. Shopify Flow, which now works with B2B objects, can add a tag automatically when an order comes from a company.
Map case-pack SKUs. If wholesale buyers order by the case, decide whether a case is its own SKU or a quantity rule on the unit SKU, and tell the warehouse how many units are in each inner and master carton. Our case pack guide covers the setup.
Set packing slip rules. Include the PO number and buyer name; decide whether wholesale prices print or are suppressed.
Set a parcel-versus-freight threshold. Pick a carton count or weight above which the order moves to LTL. Our parcel vs LTL break-even guide shows the math.
Handle ship-by dates. If buyers request a future ship date, decide where that date lives on the order and how the 3PL holds it.
Protect DTC inventory. A single wholesale order can wipe out a SKU. Decide whether to reserve stock for each channel.
Run test orders. Place a small and a large B2B test order before your first real buyer does, and check the slip, labels and carrier the warehouse chose.

Where does Shopify B2B stop and EDI start?

Shopify B2B works well for buyers who order through your store: independent retailers, boutiques, gyms, salons, cafes and corporate gifting accounts. Big-box retailers and national distributors usually do not. They send purchase orders through EDI and require you to follow their routing guide for labels, pallets, advance ship notices and appointment scheduling, with chargebacks for mistakes. That is a separate workflow, covered in our guide to retail routing guides. Many brands end up running both: Shopify B2B for long-tail wholesale and EDI for major retail accounts.

What should you ask a 3PL about Shopify B2B orders?

Does your Shopify integration import B2B orders automatically, and how do you flag them?
Can you print the PO number on slips and carton labels and suppress prices?
Who decides parcel versus LTL, and how is freight billed?
How are case-pack SKUs and inner packs set up in your system?
Can you hold an order until a requested ship date?
How are B2B orders priced compared with DTC orders?
If we add a big-box retailer later, do you support EDI and routing-guide compliance in-house?

How does Atomix handle Shopify B2B and wholesale?

Atomix connects to Shopify through the Atomix App, which brings DTC and B2B orders into one place. Wholesale batches can also be uploaded by CSV, and the app has a dedicated B2B view showing each PO's status and ship date. For retail accounts, Atomix offers EDI connections with retailers, which it describes as live in two to three weeks, plus pre-shipment checks on labels, pallets and EDI documents. Each B2B account has a named Pod Manager supported by specialists who handle routing guides, EDI and ASN requirements. See Atomix integrations for the full list of connected platforms.

Frequently asked questions

Do I need Shopify Plus for B2B?

Not anymore for the core features. Basic, Grow and Advanced include company profiles, up to three catalogs, quantity rules and payment terms. Plus adds unlimited catalogs, direct catalog assignment, partial payments and deposits.