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Phillpotts was born in Somerset and grew up in Gloucestershire, the son of a factory owner, innkeeper, auctioneer and land agent. He won a university scholarship and took his B.A. at Corpus Christi College, Oxford, and his M.A. at Magdalen College.
He took holy orders in 1802 and in 1806 became chaplain to the Bishop of Durham. Phillpotts was a prebendary of Durham from 1809. In May 1828 he became Dean of Chester, and he was appointed as Bishop of Exeter in 1830.
He was a prolific writer of articles on matters of politics, social order and religion, propounding conservative and often controversial views. He was regarded as an opponent of Catholic emancipation, and on this theme published Letters to Charles Butler (1825), Letters to Canning (1827) and A Letter to an English Layman on the Coronation Oath (1828). However, he eventually approved of Peel's scheme for granting relief to Catholics in 1829.
In the House of Lords, Phillpotts opposed the 1832 Reform Bill and most other Whig reforms. He was a high-church reformer in his own diocese, aiming to increase the prestige, efficiency and orthodoxy of the church organisation. He was well known for using litigation to achieve his aims.