The break-in happened Monday morning at the Good Shepherd Lutheran Church on north Campbell.
It was just before 6 a.m. when someone called police to report seeing a man climbing on a pole next to the church.
He was trying to get onto the roof, the caller said.
Police arrived and arrested the 45-year-old man, who was found hiding in the basement.
The suspect will be in court Tuesday and is being charged with breaking and entering.