The Duke of Rothesay will be joined by newly elected MSPs, diplomats and church leaders at St Giles' Cathedral.
The service traditionally takes place on the evening before the first sitting of a new parliamentary term. This year's ceremony includes a humanist blessing for the first time.
The Prince will meet with Holyrood's party leaders after the service.
The Reverend Calum MacLeod, minister of St Giles' Cathedral will lead the evening service, and Dr Angus Morrison, moderator of the General Assembly of the Church of Scotland, will deliver a sermon.
Guests will be greeted by music from a quartet of the National Youth Jazz Orchestra of Scotland, while musicians from the Royal Conservatoire of Scotland will perform during the service, as will the cathedral's choir.
Departing Presiding Officer Tricia Marwick, who will make a reading during the event, said it would be a "modern" service including representatives of "many faiths".
She said: "It is an honour to take part in a tradition as historic as the Kirking of the Scottish Parliament, a ceremony which was resumed when Parliament reconvened in 1999.
"It will be my pleasure to welcome His Royal Highness the Duke of Rothesay."
Humanist Society Scotland chief executive Gordon MacRae said he was "delighted" that there would be representation for non-religious people at the service for the first time.
He said: "As Scottish society changes it is only fair and proper that representatives from the large group in society that seek to lead ethical and fulfilling lives without religion are included in the country's important ceremonies."
The new session of the Scottish Parliament will formally begin on Thursday, when MSPs will be sworn in by Ms Marwick in the Holyrood chamber.
An election will then be held to choose a new presiding officer, with the formation of a government and the election of a first minister the following week.
Prince Charles is to attend an interfaith service for the Kirking of the Scottish Parliament in Edinburgh.