Percy succeeded in converting Chillingworth, and persuaded him to go to the Jesuit college at Douai, in 1630. There he wrote an account of his reasons for leaving Protestantism, but kept in touch with Laud. In 1631, however, he thought again, and left Douai. He did not immediately return to the orthodox positions of the Church of England, but was drawn into controversy with Catholics: with John Lewgar, John Floyd, and in a disputation with Thomas White before Lord Digby and Sir Kenelm Digby.His theological sensitiveness appears in his refusal of a preferment offered to him in 1635 by Sir Thomas Coventry, Lord Keeper of the Great Seal. He was in difficulty about subscribing the Thirty-Nine Articles.
As he informed Gilbert Sheldon, then Warden of All Souls College, Oxford, in a letter, he was fully resolved on two points: that to say that the Fourth Commandment is a law of God appertaining to Christians is false and unlawful, and that the damnatory clauses in the Athanasian Creed are false, presumptuous and schismatical. To subscribe, therefore, he felt would be to subscribe his own damnation. His major work was an intervention in another controversy, undertaken in defence of Christopher Potter, Provost of The Queen's College, Oxford, against the Jesuit Edward Knott. Potter had replied in 1633 to Knott's Charity Mistaken (1630), and Knott retaliated with Mercy and Truth, which Chillingworth attempted to answer. Knott brought out a premptive pamphlet tending to show that Chillingworth was a Socinian.
Chillingworth wrote The Religion of Protestants while staying at Great Tew, owned by Lucius Cary (by then Lord Falkland). Laud, now Archbishop of Canterbury, was anxious about Chillingworth's reply to Knott, and at his request it was examined by Richard Baily, John Prideaux, and Samuel Fell, and published with their approval in 1637, with the title The Religion of Protestants a Safe Way to Salvation.The main argument is a vindication of the sole authority of the Bible in spiritual matters, and of the free right of the individual conscience to interpret it. In the preface Chillingworth expresses his new view about subscription to the articles. This, in my opinion, is all intended by subscription.