 Only a small proportion of Harrison's work was on churches. In 1804 he re-faced the south side of St Peter's Church in Chester, and he carried out further alterations to the church in 1813. Between 1805 and 1806 he redesigned the nave of St John the Baptist's Church in Whittington, Shropshire, which had been badly damaged in a storm. He did design one new church, the Wesleyan Methodist Church in St John Street, Chester, which was built in 1811. Although his design was used for the exterior, the internal decoration and fittings were planned by his main contractor, William Cole, and the church has been much altered since. In 1810 came the commission for what is described as "without doubt his [Harrison's] best work at a church", to rebuild the steeple of the Church of Our Lady and Saint Nicholas, Liverpool. Earlier that year the spire on the medieval tower had collapsed, destroying the tower in the process. The work was completed in 1815 at a cost of over £ 22,000 (equivalent to £ 1,470,000 in 2015). The steeple has a height of 120 feet (37 m), its buttresses rising above the top of the tower as pinnacles, the open-work spire being supported by flying buttresses. Harrison also designed a domed ceiling for St Paul's Church in Liverpool, but this has since been demolished.
