The Church of St Stephen is one of the old town's most rewarding interiors. From outside it looks like another modest medieval church, but inside are frescoes, a carved iconostasis, and a stronger sense of the religious life that once filled the peninsula.
If you only pay to enter one church in Nesebar, make it this one or Christ Pantocrator depending on what is open. St Stephen is the better choice for interior atmosphere; Pantocrator is stronger as architecture from the street.