Under a new order, Peter McNamara from Asenby near Thirsk must pay almost £104,000 to the Diocese of Leeds.
The 71-year-old is currently serving a two-year prison sentence after being found guilty at York Crown Court in October last year of two counts of theft.
Jonathan Rowland from North Yorkshire Police 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.”
McNamara, a retired Greater Manchester Police officer, worked as an administrator at St Robert’s Church in Harrogate between May 2007 and October 2014.
Jonathan Rowland continued: “The order placed on Peter McNamara, will ensure he is prevented from having any financial gain from his shocking crime of stealing from the local church.
“The Proceeds of Crime Act 2002 is a powerful tool which allows us to demonstrate to the court how a convicted criminal has benefited financially from their crime, and then ask the court to order the money is paid 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.”
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A man who stole more than £90,000 while working as an administrator at a church in North Yorkshire has been ordered to repay the money.