In 1989 Allister became rector of St Mary's Church, Cheadle, and took on the additional position of rural dean of the Cheadle deanery in 1999. In 2001 he received media coverage when it was reported that he had refused to allow a couple to have the hymns "Jerusalem" and "I Vow to Thee, My Country" sung at their wedding. He later said:  He had previously also refused to baptise the children of unmarried parents and condemned sex outside marriage. In 1993. he wrote "Liberalism is one of Satan’s greatest weapons against the church." He attributed the fire at York Minster in 1994, the fire at Windsor Castle in 1992, and "the disastrous royal marriage saga of last year" (a reference to the separation of Charles, Prince of Wales from Diana, Princess of Wales in 1992), to the judgment of God. However, when his appointment as Bishop of Peterborough was announced in 2009, he said on the diocesan website that "his views have changed over the years and that, like all Christians, he is on a faith-journey". In 2002 Allister was appointed as the Archdeacon of Chester. In this position he has also chaired the diocesan committees on education, houses and glebe. He also acted as the bishop's adviser on healthcare chaplaincy. He became a member of General Synod in 2005 and was appointed to the commission drafting legislation relating to the possible consecration of women as bishops in 2006, serving until it delivered its proposals in 2008. On 5 November 2009 it was announced from 10 Downing Street that Allister had been nominated as the next Bishop of Peterborough. The see had become vacant with the death of Ian Cundy in May 2009. The announcement was followed by a press conference in Peterborough. The Congé d'Elire officially authorising his election as bishop was issued by Elizabeth II on 1 December 2009. He was consecrated as a bishop in St Paul's Cathedral on 25 March 2010 and was enthroned as Bishop of Peterborough in Peterborough Cathedral on 17 April 2010. On 4 November 2011, he was awarded an honorary doctorate in theology by the University of Chester "in recognition of his outstanding contribution to the promotion of Christian education". Allister is married to Janice, a general practitioner and they have three children: their son, John, is now a vicar in Nottingham.