St Nicholas, the 'Mither Kirk' of Aberdeen, named for the burgh's patron saint, dates from the 12th century and had a St Nicholas relic until the Reformation. Aberdonians didn't allow the largest parish church in Scotland to be sacked during the Reformation, locking the treasure in the Town Council. A large crucifix remained in the church until 1660.
After the Reformation the church became two separate parish churches—one meeting in each end. The two were united by the spire and north transept central chapel (now St John's Chapel of the North Sea Oil Industry). The present steeple has the largest carillon in Britain—48 bells. The two parishes united in the 1980s.
The Kirk of St Nicholas Uniting, the 2002 ecumenical partnership with the Church of Scotland and the United Reformed Church, was dissolved in 2020 and the congregation merged with Queen's Cross Church.
The East Kirk was gutted for both preservation and archeological work, beginning in 2021. The archeological dig uncovered remnants of earlier buildings and former burial sites. The East Church site is under the care of the OpenSpace Trust that is developing a fully accessible four-story building within the exterior building shell. Plans include a heritage center and restoration of the 15th century St Mary's Chapel, expected to open in 2025.
In 2024 the West Kirk was deeded to Edinburgh Palette, an arts organization with plans to create a "heritage trail," showcasing the site history and drawing tourists. The annual remembrance service for those whose lives were lost in the offshore oil and gas industry and the Kirking of the Council will continue at the site, along with other occasional services, events, and performances.