More than 800 commissioners will have the opportunity to contribute their views on September’s vote during the debate chaired by the new Moderator the Right Rev John Chalmers.
It comes after the Queen presented a letter to the opening of the General Assembly on Saturday in which she recognised the role of the Kirk in “holding the people of Scotland together” as they decide the country’s future.
The Church of Scotland is committed to a position of neutrality on the referendum but said it recognises that members have much to add to the discussion.
It said it will play a role in helping heal any divisions caused by the referendum, whatever the outcome.
In a written response to the Queen’s letter, the Church said: “We sincerely appreciate Your Majesty’s prayers for the social good of Scotland in this year of referendum.
“Whatever the outcome, we anticipate that there will afterwards be much work for the Church to do in helping people to address the consequences of the referendum and to be reconciled with each other.”
In her letter to the Assembly, the Queen said: “In this important year of referendum we pray that whatever the outcome, people of faith and people of goodwill will work together for the social good of Scotland.
“We recognise too the important role that the church can play in holding the people of Scotland together, in healing divisions and in safeguarding the interests of the most vulnerable.”
Church officials have said the debate will be a “respectful dialogue”, hearing from key speakers for and against independence before contributions are taken from the floor.
Author and lecturer Rev Dr Doug Gay, of Glasgow University, will speak for the Yes campaign with MP Douglas Alexander offering his views on the Better Together campaign.
Former Moderator of the General Assembly Alison Elliot will pose some of the questions facing undecided voters, and John Sturrock QC will sum up.
There will be no vote at the end of the debate.
The General Assembly meets for a week every year in May. It has the authority to make laws determining how the Church operates and can also act as the Kirk’s highest court.