In case you have more than one Shopify store, you can use the Multi-store feature to quickly access each account, sync new affiliates among stores, and track affiliates' performances across connected stores. This feature is only available in the Enterprise plan (you only need to have the Enterprise plan in 1 store to connect multiple stores, other stores can stay on the Free plan, however, in case you want to use advanced settings on the secondary stores, these shops must still be upgraded to paid plans).
To be specific, the Multi-store feature helps you to:
Activating Multi-store, on each shop, there will be a dropdown showing the URLs of the connected stores, you can easily select the store in the dropdown list to access other store accounts.
When an affiliate signs up to one store, the system will automatically create account(s) in the other shop(s) for that affiliate as well. There will also be a dropdown list of the connected shops in the affiliate account.
In each shop, the affiliate will have a separate affiliate link (with a unique referral code) to promote, but the ref code can work across the connected shops.
1. Go to Settings > Connect multiple stores.
2. Activate the Multi-store feature and choose a store as the main store (the main store must be using the Enterprise plan.)
3. Add other shop URLs to connect with the main stores.
NOTE: Before connecting multiple stores, in case your account has already had affiliates, you need to sync the existing affiliates to the other stores.