Jonathan Shipley was the son of a London stationer; his mother's family were owners of Twyford House, a large manor in Winchester, England. He was ordained a minister in the Church of England and became both Bishop of Llandaff and Bishop of St Asaph.
Jonathan grew up at Walbrook in the City of London. He was educated at Reading School in Berkshire. He received his college training at St John's College, Oxford, from where he received a BA degree in 1735, an MA degree in 1738, and a DD degree in 1748. He was ordained about 1738, and acted as tutor in the household of the 3rd Earl of Peterborough. In 1743, he became rector of Silchester and Sherborne St John in Hampshire, and prebendary of Winchester. He was appointed to a canonry of Christ Church, Oxford, in 1748, and in 1760 to the deanery of Winchester and the living of Chilbolton, also in Hampshire, which he held in addition to his earlier preferments.
In 1769, he was consecrated successively Bishop of Llandaff and of St Asaph. He was much concerned with politics, and joined the Whig party in strong opposition to the policy of George III towards the American colonies.
He maintained a strong friendship with the Philadelphia printer Benjamin Franklin, who stayed with Shipley in Winchester, and while there wrote much of his autobiography. In 1782, in a letter to Henry Laurens, Franklin called Shipley "America's constant friend, the good Bishop of Asaph."