In December, 1551, Dee obtained, through the offices of Mr. (afterwards Sir) John Cheke, an introduction to Secretary Cecil and to King Edward VI. He had already written for and dedicated to the King two books (in manuscript): De usi Globi Coelestis, 1550, and De nubium, solis, lunae, ac reliquorum planetarum, etc., 1551. These perhaps had been sent to Cheke, the King's tutor, in the hope that they might prove useful lesson books. The pleasing result of the dedication was the gift of an annual royal pension of a hundred crowns. This allowance was afterwards exchanged for the rectory of Upton-upon-Severn, in Worcestershire, which Dee found an extremely bad bargain.

From the Beacon Hill above West Malvern Priory, the visitor may turn from inspection of the ancient British camp of Caractacus to admire the magnificent view; and across the level fields where the Severn winds, the tower of Upton church will be seen rising in the middle distance. Further west, if the day be clear, the more imposing towers of Tewkesbury and Cloucester may be discerned, while half a turn eastward will show Worcester Cathedral, not far away. Dee never lived in this beautiful place, although he was presented to the living on May 19, 1553. Even when the rectory of Long Leadenham, in Lincolnshire, was added to Upton, the two together were worth only about £80 a year. Next year he declined an invitation to become Lecturer on Mathematical Science at Oxford, conveyed to him through "Mr. Doctor Smith" (Richard, D.C.L., 1528, the reformer), of Oriel College, and "Mr. du Bruarne," of Christ Church. He was occupied with literary work, and in 1553 produced, among other things, a couple of works on The Cause of Floods and Ebbs, and The Philosophical and Political Occasions and Names of the Heavenly Asterismes, both written at the request of Jane, Duchess of Northumberland.

When Mary Tudor succeeded her young brother as queen in 1553, Dee was invited to calculate her nativity. He began soon after to open up a correspondence with the Princess Elizabeth, who was then living at Woodstock, and he cast her horoscope also. Before long he was arrested on the plea of an informant named George Ferrys, who alleged that oneof his children had been struck blind and another killed by Dee's "magic." Ferrys also declared that Dee was directing his enchantments against the Queen's life. Dee's lodgings in London were searched and sealed up, and he himself was sent to prison. He was examined before the Secretary of State, afterwards upon eighteen articles by the Privy Council, and at last brought into the Star Chamber for trial. There he was cleared of all suspicion of treason, and liberated by an Order in Council. August 29, 1555, but handed over to Bishop Bonner for examination in matters of religion. Bonner was apparently equally satisfied. Dee was certainly enjoined by him, at John Philpot's examination on November 19, 1555, to put questions as a test of his orthodoxy. He quoted St. Cyprian to Philpot, who replied: "Master Dee, you are too young in divinity to teach me in the matters of my faith, though you be more learned in other things."