Stephen and Jayne Pagan said they were shocked and appalled that someone had broken into a donations box at Dornoch Cathedral just weeks before Christmas.
They described the theft as "gut wrenching" for a small place that worked hard to support local people and the wider community.
According to the Church of Scotland, a thief broke into a locked Perspex donations box on Friday.
Three women had stored £350 there the day before for safekeeping but the total sum of money taken was likely higher.
Mr Pagan said he and his wife, who run The Steading guesthouse at Balnapolaig, Dornoch decided to replace the £350, partly in memory of his late sister-in-law, Sonje Marshall, who died earlier this year at the age of 50.
Sonje, who had Down's Syndrome and advanced dementia, regularly attended Dornoch Cathedral and its Common Ground group, which supports Adults with disabilities.
Mr Pagan said: "I felt a huge pain in my heart when I heard what had happened.
"It was almost like someone had died because this kind of thing tends not to happen in Dornoch.
"It was gut wrenching really and we couldn't believe that someone would steal from a church at Christmas which is a time for giving not taking.
"We immediately said to each other 'lets find out how much is missing' and just replace it because we knew that a lot of people who worked hard to raise it would be feeling bad.
"Sonje was very much involved in the life of the Cathedral and we knew that she would have wanted to do something about it as well."
The money had been raised to pay off loans and bills owed for the refurbishment of the West Church Hall.
Minister, Rev Susan Brown, the Moderator Designate of the General Assembly, said she was "really touched" by the couple's gesture and described them as "special" people.
Mrs Brown, who conducted Ms Marshall's funeral in March, said she had received more than 500 messages of support from people following the theft.
