CCTV caught a person in a hoodie and baseball cap breaking into the rooms behind the church on Sunday morning and leafing through their items.
He stole five bank cards, mobile phones, an apple laptop and cash.
He had entered All Saints Northampton in time for the morning service and received a "hymnbook and a warm welcome" according to director of music, Jem Lowarth.
Mr Lowarth, 27, was in the church at the time and told Premier: "Our service started at 10.30, it ended around 11.45 and it was pretty quickly after that the choir members started reporting that some of their things were missing.
"We were singing, taking part in the liturgy as we do every single Sunday...I was playing the organ, I was playing the first hymn while the events took place.
"A nine year old girl was particularly upset, especially at the beginning. She was obviously sad she lost her things. She was also worried that parents would be angry at her for having lost them, which, of course, wasn't the case."
Mr Lowarth explained that the culprit seemed to have been checking out the church for a few days.
"He'd been hanging around the church, I was told, on Saturday - and earlier in the week - and actually on Sunday he was in the church. Before the service, he was handed the service leaflets and a hymn book and, seeing the choir process in, seeing the first hymn, was his hint that the choir rooms upstairs were not occupied.
"He was given a warm welcome at the back of the church. We don't challenge people as to their identity or their intention when they walk into church on a Sunday morning to join a service but he was given the same welcome we give every single person and as it happens, he was just using this as a pretext to force his way into our rooms and see you for members of our choir."
The choir room was locked and the door was forced open with a tool.
All Saint's Church rector Father Oliver wrote on Facebook: "We have a commitment to being an open church, and do not shut our doors simply because of incidents like this. Our general experience is, in any case, that locked doors do not deter the determined and desperate criminal. And so, as Christians called and sent we must get on with the business of loving our neighbour, and praying for those who persecute us (Matthew 5: 44),
"We hope that the desperate state our burglar finds himself in might be the door to a different life."
Stay up to date with the latest news stories from a Christian perspective. Sign up to our daily newsletter and receive more stories like this straight to your inbox every morning.