In general, we’ve seen people using solutions like Branch.io and Appsflyer for deep linking from their email messages vs. other messaging channels. However, currently only Branch.io has an integration with Customer.io. You can read about the integration here.

If you want to track deep links from your emails and you’re not using Branch.io, it’s necessary to use the Universal link process outlined in this Customer.io Docs article. TL;DR, you’ll need to include the special Liquid tag {% cio_link_id %} along with the universal link. Then your app will be responsible for posting the link click back to Customer.io with that same id.