Peter McNamara, 71, from Asenby near Thirsk, worked as an administrator at St Robert’s Church and the attached conference centre between May 2007 and October 2014.
He is currently serving a two year prison sentence after being found guilty of two counts of theft at York Crown Court in October 2018.
He appeared at the court again last week under the Proceeds of Crime Act 2002.
A judge told him that he would have to pay back a total of £103,711.56 to the Diocese of Leeds.
The news has been welcomed by North Yorkshire Police's Economic Crime Unit.
Speaking about the decision today, Acting Detective Inspector Jonathan Rowland said: “Whilst securing a conviction and sentence is vital in these cases, so is the follow up work that goes on after criminal court proceedings.
"North Yorkshire Police, wherever possible, will seek to use available legislation in order to redress the financial damage done to a victim.
“The order placed on Peter McNamara, will ensure he is prevented from having any financial gain from his shocking crime of stealing form the local church. If he fails to pay what he owes, he will once again be put before the courts."
He said the Proceeds of Crime Act 2002 was a powerful tool allowing police to demonstrate to the court how a convicted criminal has benefited financially from their crime and ask for the money back.
"Our Financial Investigators work hard to ensure that in every case where it is possible for money to be paid back, it is put before a judge for consideration,” he added.