The sisters of Santa Ines in Seville, southern Spain, accepted the offer from a local charity to restore the instrument for free.
Abbess Blanca Cervantes defended the nun's decision and told the ABC de Sevilla newspaper: "It hasn't worked for 30 years, and we couldn't afford the estimated cost of more than 150,000 euros (£135,000).
"We only make enough money from the sale of sweets to cover our bills and national insurance payments."
Unbeknown to them, their actions could be considered a criminal offence.
The regional government of Andalusia fined the convent 170,000 euros for the "unauthorised" work on the organ.
It has, however, said it will let the charity finish the restoration work in time for Christmas.
The organ was built by 17th century Perez Valladolid before Andalusia's Ministry of Culture listed it as an Item of cultural significance in 1983.
While the ministry insists it is simply applying the law, according to the BBC, it is willing to show mercy to the nuns by offering to cut the fine to102,000 euros if they settle and pay outside of court.
The Alqvimia Musicae Foundation that funded the restoration insists the nuns will not have to pay out of their own pockets, and is planning a charity lunch to raise money for the fine on Sunday.
