Kate Middleton, Prince William and Prince George were among the congregation at the baptism, during which Kate became godmother to a close friend's baby.
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There were 50 people at the service, where the Duchess was one of four godparents who promised to support and guide the little boy throughout his spiritual life.
The church was still open to regular parishioners, many of whom were taken aback to see the royal visitors in attendance.
Reverend Ken Dunstan told the Daily Mirror: "I think my usual congregation were surprised at who was joining us.
"My main concern was that I got the tone right for the family and for the baptism.
"I don't normally pay a huge amount of attention to godparents as long as the godparents are there and willing to make the appropriate promises."
Of Kate, he said: "She was there as a godparent not as a princess."
Kate and William with Prince George at his christening in October
The mother of the little boy was a friend of the Duchess' from her days at St Andrew's University.
Reverend Ken said: "The couple said they wanted four godparents but weren’t quite sure whether one would be available.
"Then later the father rang me to say the other godmother is available, it's a friend from uni.
"Then he told me who it was. I got the impression that a number of the congregation had been to the same university."
According to the Reverend, Prince George was good as gold during the baptism. "There were several babies present and all were very well-behaved," he said.