The man was found Dartmouth Apprentice site, in Dartmouth, on Saturday evening. Two men were arrested and are being held at Torquay Police Station, officers said.
The 1830s St Barnabas Church building is now a supported living project.
Devon and Cornwall Police said the man was treated by paramedics, but later died.
The building was a church until 1973.
A murder inquiry has started after a 48-year-old man found injured at a former church building in Devon died.