Integrations

Shopify inventory management for wholesale and D2C food brands

Last updated: 16 October 2026

Shopify runs a D2C store well, and since April 2026 its core B2B features are on Basic, Grow and Advanced plans. It doesn't read a Sainsbury's PDF or an EDI file, and batch, use-by and FEFO tracking need apps. Pesto takes your Shopify orders alongside retailer and wholesale orders, allocates stock by batch and routes each order to your 3PL.

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Pesto sales orders list with the Source filter open, listing each channel orders can arrive from

What does Shopify do well for food brands?

Shopify is the default for D2C, and for good reason. Your storefront and checkout run there, and your team already knows it.

Shopify B2B has also moved down the plans. Since 2 April 2026, core B2B features sit on the Basic, Grow and Advanced plans:

Company profiles

For each trade customer

Payment terms

Volume pricing

Up to three B2B catalogs

Unlimited catalogs, deposits and partial payments stay on Shopify Plus.

Shopify's core inventory tracks quantities per location. If you sell online from one warehouse, that covers a lot.

Where does Shopify stop for food brands selling to retailers?

The gaps appear when your sales stop being only D2C.

Retailer orders.

Shopify doesn't read a Sainsbury's PDF or an EDI file. Third-party apps exist, but out of the box, someone retypes the PO.

Batches and use-by dates.

Batch and lot tracking, expiry dates and FEFO need apps on top of Shopify's core inventory.

Customer-specific pricing at scale.

Three B2B catalogs on the non-Plus plans run out quickly if each wholesaler has its own agreed price list.

Stocky has gone.

Shopify retired Stocky, and it stopped working on 31 August 2026.

None of this makes Shopify the wrong choice for your store. It means your store isn't the whole business once Ocado, a wholesaler and a dozen delis are ordering too.

How does Pesto work with Shopify?

Install the Pesto Shopify app and Shopify becomes one more order channel in Pesto, with its own product list.

Product mapping, suggested for you.

Pesto's AI suggests a match for each Shopify product, by barcode first, then SKU. You confirm the matches once.

Nothing slips through unmapped.

If a Shopify order includes a variant Pesto hasn't mapped, Pesto holds it for review rather than processing it.

One queue for every channel.

Shopify orders sit beside your EDI, PDF and email orders, so you see every order in one place.

Stock taken by batch.

Switch on Shopify auto-deduct and Pesto takes stock when Shopify fulfils an order, using FEFO (first expired, first out) from one location you choose. Your allocation rules still apply.

Routed to your 3PL.

Routing rules can send Shopify orders to your 3PL, the same way they route your wholesale orders.

Clear invoice status.

Orders Shopify has already invoiced show as "Invoiced (Shopify)", so you can tell them apart from orders you invoice through Xero.

Your Shopify store keeps selling. Pesto keeps the stock behind it accurate.

Pesto Shopify settings showing product mapping, unmapped variants held for review and FEFO stock deduction — Unmapped Shopify variants are held for review, not processed

How does Pesto handle wholesale and retail orders alongside Shopify?

This is the part Shopify doesn't do, and it's where Pesto earns its place.

Retailer EDI.

Orders from Ocado, Sainsbury's and other UK retailers arrive through your EDI system (e.g. TrueCommerce, Supply Lens, XEDI).

PDFs, spreadsheets and emails.

Upload or forward a PO in any common format, and Pesto pulls out the customer, depot, lines, quantities and prices.

Your customer's own codes.

Pesto matches each line to the customer's own product code and finds the depot by GLN, then postcode. We call this order normalisation.

Agreed prices.

Pesto fills missing prices from each customer's price list or tier and flags any mismatch with "Expected: £x".

Shelf-life rules per customer.

Set a minimum shelf life per customer and choose Allow, Warn or Block when a lot falls short.

Delivery notes with batch codes.

Every line carries the batch code and use-by.

A B2B ordering portal.

Independents and wholesalers can order from a branded, passcode-protected shop that shows each buyer their own catalogue and prices.

→ Order management · → Inventory

Who should stay on Shopify alone?

If you sell only D2C through your own store, ship from one warehouse and no customer asks you for batch codes, or minimum shelf life, Shopify and your 3PL cover it. You don't need Pesto yet.

Pesto starts to pay off when:

a retailer or wholesaler sends you POs as PDFs, spreadsheets or EDI
your buyers check batch codes and use-by dates on delivery
your stock sits in more than one place, or with more than one 3PL
someone on your team spends their Monday morning retyping orders

That's usually the point a challenger brand lands its first big listing. → Brands that buy finished goods

Order management

Shopify, EDI, PDF and email orders in one review queue.

Inventory

Batch codes, use-by dates, FEFO and shelf-life rules.

Xero integration

Invoices from what you dispatched, synced back to Pesto.

→ See all integrations

Frequently asked questions

Can Shopify track batches and expiry dates?

Not in its core inventory, which tracks quantities per location. Batch and lot tracking, expiry dates and FEFO need apps. Pesto records every lot with its batch code, use-by and location, and allocates by FEFO.

Is Shopify B2B enough for selling to supermarkets?

Shopify B2B works for trade buyers who order online. Supermarkets send POs by EDI or as PDFs, and Shopify doesn't read a Sainsbury's PDF or an EDI file. Pesto takes those orders through your EDI system (e.g. TrueCommerce, Supply Lens, XEDI), or straight from the document.

What happens if a Shopify product isn't mapped in Pesto?

Pesto holds the variant for review rather than processing it. Map it once and Pesto matches it on every future order.

Does Pesto take stock off when Shopify fulfils an order?

Yes, if you switch on Shopify auto-deduct. Pesto takes stock by FEFO from one location you choose, and your allocation rules apply.

Can Pesto send Shopify orders to my 3PL?

Yes. Routing rules send Shopify orders to your 3PL, alongside your wholesale and retailer orders.

Do I need Pesto if I only sell D2C?

Not yet. If Shopify is your only channel and nobody asks for batch codes or shelf life, Shopify and your 3PL are enough. Come back when your first retailer PO lands.

See Pesto running on your own orders.

Bring a real PO, your messiest one. We'll show you what Pesto does with it in 30 minutes.

Book a demo

Sources

Shopify changelog, key B2B features now available on non-Plus plans, 2 April 2026. https://changelog.shopify.com/posts/key-b2b-features-now-available-on-non-plus-plans
Shopify Help Center, B2B features by plan, accessed October 2026. https://help.shopify.com/en/manual/b2b/getting-started/plan-features
Shopify blog, perishable inventory management, accessed October 2026. https://www.shopify.com/blog/perishable-inventory
Shopify, Stocky retirement (stopped working 31 August 2026).