On 10 June 2006, Lincoln married Gael Anderson, daughter of Ian Anderson, former flutist and vocalist in Jethro Tull. They have two children, Matilda and Arthur.[33] Apple Martin (daughter of Gwyneth Paltrow and Chris Martin) was the flower girl at their wedding.[6]
Lincoln's older brother, Richard Clutterbuck, was formerly head of the Bristol Free School[34] and is the current head of Kings Oak Academy in Kingswood.[35]