Lancashire Police said officers found about 1,000 cannabis plants, with an estimated street value of £650,000, on Monday in the main hall of the building in Parkgate Drive.
Detectives said the plants were spread over three storeys of the former St Michael's Church and had been split into 12 different rooms.
The building has now been partially converted into flats.
A 24-year-old man was arrested on suspicion of cultivating cannabis and is currently being questioned.
Detective Sergeant Martin Foley said: "We know the misery drugs can bring to a community and we are determined to do everything we can to remove them.
"We rely on the public's continued support and I urge anyone with information or concerns to contact us."