The Reverend Scott Rennie will be introduced to his congregation at a service at Queen's Cross Church.
Hundreds of ministers and thousands of Church of Scotland members signed an online petition opposing the appointment.
The issue went to the General Assembly which narrowly voted in favour.
But there has been a two-year ban on the ordination of gay ministers and a special commission is considering the issue.
Robert Pigott
BBC's religious affairs correspondent
Scott Rennie, who has been a minister for 10 years, had a child with his former wife but now lives in an openly gay relationship.
His appointment as minister at Queen's Cross Church in Aberdeen was denounced by traditionalists who insisted that the Bible clearly outlawed active homosexuality.
About 400 ministers and 5,000 church members signed a petition against the appointment, and an attempt was made at the church's General Assembly to overturn it.
The assembly approved Mr Rennie's appointment, but then imposed a two-year moratorium on the ordination of gay clergy while a specially convened group considered
the issue.
As the assembly met to debate the issue, Mr Rennie said other instructions in the Bible - such as those about stoning adulterers - were no longer followed, adding
"we've moved on from that".
He has been open about his relationship with his partner and plans to live with him in the manse in Aberdeen.
Some sections of the Church of Scotland feared Mr Rennie's appointment could cause the greatest divide since the Disruption of 1843, when part of the Kirk broke away to form the Free Kirk.
Mr Rennie had been backed by the majority of the congregation at Queen's Cross Church.
A spokeswoman for Aberdeen Presbytery said: "I think everything is more settled now.
"The congregation want Scott to be their minister and I'm sure they're now just ready to get on with things."
The induction ceremony at the west end church, at 1900 BST, will be led by the Rev Alan Falconer.
The spokeswoman said: "Towards the end of the service, Scott will be asked to take vows about his beliefs. Thereafter, he'll be the minister."
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