A gang broke into Prestonkirk church in East Linton, East Lothian, where they are believed to have played the instrument before forcing open the organ chamber and stealing several pipes, leaving others bent out of shape.
Nothing else was damaged within the ancient church, but to add insult to injury, beer bottles were smashed inside the mechanism.
Reverend David Scott, the minister in charge of the Parish of Traprain, which includes Prestonkirk, said: "The attack was focused on the organ pipes. Some were stolen, others were deliberately bent.
"The door to the organ chamber was forced open. Two Budweiser beer bottles were found in the mechanism - one was smashed.
"The organ had been switched on, stops were out and the organist's music was strewn on the floor."
The organ, by Vincent of Sutherland, was only overhauled in 2004 and the damage is expected to amount to more than £7,000.
The vandals struck some time between 11pm last Wednesday and the following Thursday morning.
Rev Scott said police had recovered DNA samples from the beer bottles and fingerprints from the door.
Inspector Ian Mackay of Police Scotland said: "Anyone with information that can assist with our inquiries is asked to contact police on 101."