The plan was revealed in the reply approved by the Church of Scotland’s General Assembly to the Queen’s traditional letter of greeting read at the Assembly’s opening session on Saturday.
The reply also assured the Queen of the Kirk’s prayers following the death of the Duke in April at the age of 99, the longest-serving consort of a reigning British monarch.
Former Moderator the Very Rev Dr Martin Fair, who handed over the role to Lord (Jim) Wallace of Tankerness at the start of this year’s Assembly, read out the reply for the Assembly’s approval.
It said: “Your Majesty has been continuously in our thoughts since the passing of the Duke of Edinburgh.
"We know that you will have been sustained by your Christian Faith yet your loss will have been keenly felt and we wish to assure Your Majesty that many people in the Church of Scotland and beyond have prayed for you and members of the Royal Family in these testing times.
“In due course, and when pandemic restrictions allow, we will gather in St Giles’ Cathedral to give thanks for the Duke’s life and his contribution the nation of Scotland.”
The reply went on to thank the Queen for her “concern and prayers for the people of this land as they have journeyed through the pandemic”.
And it said: “These have indeed been difficult days shadowed by illness, bereavement, unemployment and economic damage. We would want to humbly acknowledge Your Majesty’s steadfastness throughout these troubled times – leadership that has never been wanting throughout the years of your reign. We have sensed always your desire to serve and in that we are minded that Our Lord came not to be served but to serve.”
Prince William is attending the Assembly as this year’s Lord High Commissioner, the Queen’s representative, and in his address at the opening session he spoke of the royal family’s love of Scotland and his own memories, including the “saddest” when he was told of his mother’s death while staying at Balmoral.