Hi @Kylie.C, 

Welcome to the Community! Thanks for sharing your question with us, 

You can definitely still send transactional emails after migrating to your own eCommerce platform instead of Shopify. However, you will need to set this up via API to send a Klaviyo transactional email when a customer triggers this action. I recommend checking out this. thread with a similar situation to gain more insight! 

Finally, you will still need to reach out to Support to activate these emails and turn them live. I’d also suggest reading this thread as well that talks through how to create these emails via API. 

Thanks for participating in the Community!

-Taylor