Emergency services were called in scene of the incident on Pearl Street in the Splott area of the city shortly before 3pm yesterday.
According to South Wales Fire and Rescue Service, two people escaped with minor injuries while a third person found trapped in the rubble died.
Area manager, Gareth Davies said: "A gentleman was sadly found trapped within the collapsed structure and has tragically lost their life.
"As a Service, we wish to extend our sympathies to the individual's family at this very sad time."
Trains on the nearby Cardiff to Newport railway line operated with a restricted timetable as a precaution in response to the incident.
It is understood the church building which collapsed was set to be demolished. Pictures show scaffolding had been errected on the site.