Two other people escaped from the building in Cardiff with minor injuries.
The church was adjacent to a railway track leading to services being suspended between Cardiff and Newport.
Local demolition firm Young Contractors had been working on the church for about three weeks.
The firm told the BBC that none of its staff were on site at the time of the tragedy.
South wales Fire and Rescue said: “A man was sadly found trapped within the collapsed structure and tragically lost his life.”