Since SEPA transactions have multi-level authentication, they already meet the standards set by the SCA. Hence all SEPA transactions are exempted from the 3DS. Also, transactions going through Paypal Express checkout and Amazon Payments are exempted for the same reason. 

If you wish to know more about 3DS and how Chargebee is handling it, then please click on the link below.

https://www.chargebee.com/resources/guides/psd-2-sca-for-saas/