Fire crews arrived at Guildford Methodist Church on Woodbridge Road in Surrey at around 7am, after rubbish was thought to have ignited.
Crews from Guilford, Woking and Camberley were called, and Watch Commander Edwards from Guildford fire station said: "We received reports of a fire at the church.
"As we arrived we were met at the front by one of the people using the place as a squat."
"We have gone into the premises. There was heavy smoke as we entered.
"The source of the fire is thought to have been in a pile of rubbish.
"There's heavy smoke damage in the back corner of the premises. The fire started on the stage and dropped down below.
"We have a fire investigator on his way at the moment but we believe it was accidental."
There were no reported injuries and the area was cordoned off as fire-fighters dealt with the blaze.
Earlier this year, a building company, Shanley Homes, lost an appeal to demolish the church, after it had been vacant for around 18 months.
