An episode of the show is scheduled to be recorded at the cathedral on 5th March but a local choir has been asked to perform, not Bangor Cathedral choir.
While Cor Glanaethwy choir was chosen to perform on the show, the cathedral's choir was invited to sing as part of the congregation.
According to BBC News, the decision angered some members of Bangor Cathedral choir, which include children and adults.
One of the children, who asked to remain anonymous, wrote a letter to the cathedral describing the actions of Songs of Praise as "disrespectful".
The child wrote: "Songs of Praise is a Christian television programme, and cathedral choir is a Christian choir.
"Yet the choir has not been asked to sing in Songs of Praise, which is a snub to the choir."
A parent of one of the singers has written to the cathedral's governing body claiming that the cathedral choir has been teased by singers from Cor Glanaethwy at school over the situation.
Very Rev Kathy Jones, Dean of Bangor Cathedral said: "We are delighted that Songs of Praise are going to be recording at Bangor Cathedral and that a number of groups from the community are taking part."
A BBC spokesperson added: "Songs of Praise films in different cathedrals across the UK often working with a number of choirs in a location and on this occasion, we are filming with Ysgol Glanaethwy.
"All the local choirs, including the Bangor Cathedral choir, have been invited to be part of the congregation singing the hymns."
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