The Greyfriars' Chronicle says that Hooper was "sometime a white monk"; and in the sentence pronounced against him by Stephen Gardiner he is described as "olim monachus de Cliva Ordinis Cisterciensis," i.e. of the Cistercian house of Cleeve Abbey in Somerset.

On the other hand, he was not accused, like other married bishops who had been monks or friars, of infidelity to the vow of chastity; and his own letters to Heinrich Bullinger are curiously reticent on this part of his history.

After some correspondence with Bullinger on the lawfulness of complying, against his conscience, with the established religion, and following some trouble in England c. 1539–40, with Stephen Gardiner, bishop of Winchester to whom Arundell had referred him out of concern for his new views, Hooper determined to secure what property he could and take refuge on the continent.

[1] After living in Paris for an unknown period of time, Hooper returned to England to serve Sir John St Loe, constable of Thornbury Castle, Gloucestershire, Arundell's nephew.

There, he became the principal champion of Swiss Calvinism, against the Lutherans as well as the Catholics, and was appointed chaplain to Edward Seymour, 1st Duke of Somerset, the Lord Protector.

Confinement to his house by order of the Council proved equally ineffectual, and it was not until he had spent some weeks in the Fleet prison[6] that the "father of nonconformity" consented to conform, and Hooper submitted to consecration with the legal ceremonies (8 March 1551).

[7][1] Though Hooper had a low view of the role of bishops in the church, he soon set about a visitation of his diocese, which revealed a condition of almost incredible ignorance among his clergy.

[1][9] Following examinations of 311 clerics, 168 were not able to repeat the Ten Commandments, and 31 were unable to state in what part of the Scriptures they were to be found; there were 40 who could not tell where the Lord's Prayer was written, and 31 were ignorant of who authored it.

He wrote to William Cecil pleading for the council to take action on the price of essential goods, for "all things here be so dear that the most part of the people lack ... their little livings and poor cottages decay daily.

It was this form of religion that he laboured to spread in England and with others, such as Nicholas Ridley, Martin Bucer, and Pietro Martire Vermigli, he influenced the changes in the 1552 edition of the Book of Common Prayer.