If you sell on Shopify and do your accounting in Xero, you already know the drill: order comes in, you (or someone on your team) manually creates an invoice. Multiply that by every order, every day — it adds up fast, and so do the mistakes.
Wherehouse's Shopify → Xero integration changes that. Every order that lands in your Shopify store is automatically turned into a Xero invoice — with the right contact, the right line items, the right account codes, and the right tax treatment. No copy-paste, no missed fees, no end-of-month scramble.
Who goes on the invoice?
One of the first questions sellers ask is: "Does every Shopify customer become a new Xero contact?" The answer is: it depends on what works best for you.
By default, Wherehouse pulls the buyer's name, email, phone, and address directly from the Shopify order and builds a Xero contact on the fly. Xero will auto-match returning customers — so you naturally build up a real contact list over time.
If you'd prefer a cleaner books setup — say, all Shopify orders billed to a single "Shopify Store" contact — you can pin invoices to a specific Xero contact ID using Wherehouse's field mapping. This is popular with wholesale and B2B sellers who don't need individual buyer contacts in Xero.
You can even use field mapping to set different contacts based on order attributes — for example, routing wholesale orders to a wholesale contact and D2C orders to individual buyers.
What goes on the invoice?
A Xero invoice created by Wherehouse isn't just a single line that says "Shopify sale." It's a full breakdown of everything on the order — structured exactly the way your accountant expects it.
Products
Each product line maps to a Xero item by SKU. That means the invoice line is linked to the item in your Xero catalogue — unlocking sales analytics, COGS tracking, and inventory reports inside Xero. If a product doesn't have a matching Xero item yet, you can configure it to post as a simple account-code line instead, so invoices never get blocked.
Shipping
Shipping is added as its own line item, with the carrier or method name from Shopify as the description. It posts to a dedicated shipping account code (default: 201, but fully configurable).
Fees & discounts
Transaction fees and order discounts are included as separate line items — fees posting to a fees account code, discounts as negative lines at the bottom of the invoice. You can also choose to apply discounts inline (reducing the unit price) or disable fees/discounts entirely if they're not relevant to your setup.
Discount lines are always sorted to the bottom of the invoice automatically, keeping the invoice easy to read.
Refunds? Sorted.
When a Shopify order is refunded, you don't want to manually raise a credit note in Xero. Enable the returns option in Wherehouse and it handles it for you.
Whether it's a full refund, a partial refund, or a cancellation — Wherehouse detects the change and creates a matching ACCRECCREDIT credit note in Xero against the same contact, with the refunded product lines and shipping. And because it deduplicates by reference, you'll never end up with double credit notes even if the sync runs multiple times.
Configure it your way
No two sellers run their books the same way. Wherehouse is built to be configured, not constrained.
Here's a snapshot of what you can control:
- Account codes — set a specific Xero account for sales, shipping, fees, discounts, COGS, and inventory asset accounts.
- Tax treatment — send prices as tax-inclusive, tax-exclusive (15% VAT is stripped before sending), or with no tax at all.
- Invoice status — choose whether invoices arrive in Xero as Draft, Submitted, or Authorised.
- Due date — configure how many days after the order date the invoice is due.
- Branding themes — apply a custom Xero branding theme to your invoices.
- Tracking categories — automatically tag every invoice line with a Xero tracking category and option, great for channel-level reporting.
- Fee handling — post fees as a rolled-up account-code line, or as individual line items attached to each product.
- Product linking — link invoice lines to Xero items for analytics, or use simple account-code posting for a lean Xero items list.
Product & inventory sync
The integration isn't just about invoices. Wherehouse can also keep your Shopify product catalogue and your Xero items in sync.
- Push products out — when a product is created or updated in Shopify, Wherehouse creates or updates the corresponding Xero item, including sales price, cost price, and account codes.
- Pull items in — import your Xero items back into Wherehouse and push their prices and stock levels out to your other channels.
- Tracked inventory — optionally mark Xero items as tracked inventory. Wherehouse will configure the right COGS, purchases, and inventory asset account codes automatically.
Getting started
Connecting Shopify and Xero in Wherehouse takes a few minutes. You'll authorize both platforms, configure your account codes and preferences once, and from that point on it runs hands-free.
We will always post example invoices to DRAFT status before going live with your integration, meaning you will have the opportunity to check the business logic set up before things start pushing through automatically.
Our onboarding team can walk you through the configuration for your specific accounting structure.
Ready to connect Shopify and Xero?
Wherehouse connects your Shopify store to Xero in minutes. Tell us which platforms you use and we'll set up the right integration for your business — invoices, credit notes, product sync, and all the configuration options covered above.
- Connect Shopify — your orders, products, and customer data
- Connect Xero — your accounting organisation and chart of accounts
- Pick your setup — contact mapping, account codes, tax treatment, and more
Get started at wherehouse.co.za — select Shopify and Xero when you fill in the sign-up form and we will get your integration configured.
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