Officers found around 1,000 cannabis plants in the main hall of the church on Parkgate Drive around noon on Monday January 11.
The plants were spread over three storeys and divided into 12 growing rooms in the building which has now been partially converted into flats.
A 24-year-old man was arrested on suspicion of cultivating cannabis and is currently being questioned by police in Lancaster.
DS Martin Foley of Lancaster Intelligence Department 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.”
Anyone with information about drugs can contact police on 101 or Crimestoppers anonymously on 0800 555 111.
A warrant was also executed on the Marsh estate, where a man from Liverpool was found to have a package containing about 150 wraps of heroin and crack cocaine.