If you sell to multiple countries using Shopify Markets and run more than one business entity, you might want each entity’s Shopify sales and payouts to go to a separate Xero or QuickBooks company.
This article explains:
What’s possible today with Shopify Markets and Link My Books
When you can send settlements to different accounting files
What we need from you to set things up for your store
This guide is for both ecommerce brands and accountants working with Shopify stores.
What you can achieve with this setup
With the right Shopify configuration, Link My Books can help you:
Send the right settlements to the right accounting file, for example:
US sales and payouts → your US Xero/QuickBooks company
UK and EU sales and payouts → your UK Xero/QuickBooks company
Keep clean, separate books per legal entity, even when you sell from a single Shopify store
Reduce manual journal adjustments and reclassifications at month‑end
If you manage multiple entities under one brand, this can make your reporting, tax, and year‑end work much easier.
What you need in Shopify
To route settlements to different accounting files, Shopify needs to clearly separate each business entity for you.
You’ll typically need:
Multiple business entities in Shopify
Set up each company (for example, your UK Ltd and your US LLC) in Shopify.Shopify Payments configured for each entity
Each entity should have its own Shopify Payments onboarding and payout details.Markets mapped to entities
Make sure the right markets/regions are linked to the right entity in Shopify.
Shopify’s guide on selling with multiple entities is a good starting point:
Selling with multiple entities
If you’re unsure whether your store is set up this way, your Shopify admin or accountant can check, or you can share this link with them.
How Link My Books can help once Shopify is ready
When your Shopify store is set up with multiple entities as above, Link My Books can:
Connect each entity’s settlements to the correct Xero/QuickBooks company
Keep sales, fees, refunds, taxes and payouts separate per entity
Follow your existing Link My Books mappings and rules, per accounting file
From your point of view, this means:
Your US books only show the activity that belongs to your US entity
Your UK books only show the activity that belongs to your UK entity
Your accountant doesn’t need to untangle mixed settlements every month
What we need from you
Once your Shopify setup is ready, we’ll help with the Link My Books side.
When you contact Support, please include:
Your Shopify store name / myshopify URL
Which accounting platform you use: Xero or QuickBooks
The names of the accounting files you want us to use (for example, “Company Name LLC (US)” and “Company Name Ltd (UK)”)
Which markets/regions should post to each accounting file (for example, US + CA → LLC, UK + EU → Ltd)
A list of your payment methods (for example: Shopify Payments, PayPal, Klarna, Clearpay)
With that information, we can confirm what’s possible for your specific setup and complete the configuration.
If your Shopify store uses a single entity
Many merchants use Shopify Markets but still operate a single legal entity in Shopify.
If your store is set up this way:
Shopify will treat all your sales and payouts as belonging to one entity
Link My Books will send all Shopify settlements to one accounting file
You can still use all the usual Link My Books features (auto‑posting, country/currency analysis, etc.), but settlements will not be split by entity.
If you plan to move to a multi‑entity structure in future, your accountant can help you:
Update your Shopify configuration, and
Decide when to start routing settlements into a second accounting file
Need help deciding what’s possible?
If you’re not sure whether your Shopify store can support multi‑entity posting:
Share this article with your accountant or Shopify admin, or
Contact Support with your Shopify URL and a short description of how your business is structured (for example, “one UK company and one US company”)
We’ll review your setup and let you know the simplest option to keep your books clean across entities.