His first task was the organisation of the church in Tasmania, and being a moderate high churchman he came into conflict with some clergy of evangelical views.
His Lectures, Historical, Doctrinal, and Practical on the Catechism of the Church of England, a volume of over 600 pages, was published in London in 1843, and a second edition was called for in the following year.
Endeavouring to act on his letters of appointment, he came into conflict with the governor, John Eardley-Wilmot, and the Presbyterian and other denominations petitioned Queen Victoria on the subject.
Nixon's administration of the Diocese of Tasmania was firm and energetic, and he set a good example to the colonists by devoting a large proportion of his own income to the needs of the church and education.
In addition to the works already mentioned Nixon published a short History of Merchant-Taylors' School in 1823, The Cruise of the Beacon, A Narrative of a Visit to the Islands in Bass's Straits (1857), and some charges and sermons.