Vermigli's share in the preparation of the prayer-book of 1552 has been variously estimated, but seems to have been limited to advocacy of alterations proposed by Bucer before his death. These changes were in some instances adopted; other objections were met by emendations made by English bishops, especially Ridley. Vermigli was placed on the commission (11 Nov. 1551) of eight (six divines and two laymen), selected from a larger commission (6 Oct.) of thirty-two, for reformation of the ecclesiastical laws (Cardwell, Documentary Annals, 1839, i. 95). He came up to London as Cranmer's guest at Lambeth. The new code had already been drafted in the previous reign, under Cranmer's superintendence; it was now revised by Cranmer and Vermigli, the phraseology being corrected by Walter Haddon, LL.D. [q. v.], and was published in 1571, 4to, but never authorised (see Cardwell's reprint, 1850, with information based on Harl. MS. 426, containing great part of the original). Vermigli returned to Oxford on the dissolution of parliament (15 April). The Strasburg authorities were anxious for his return thither; but Edward VI would not permit it.
Early in 1553 Vermigli's wife died of fever, and he was for some months prostrated by the same disorder. On the accession of Mary he was kept prisoner in his house for six weeks, Henry Siddall or Syddall [q. v.] being charged to prevent his escape. His friend Terenziano, with William Whittingham [q. v.], petitioned the privy council at Richmond for a license enabling him to leave the kingdom. Through the interest of Sir John Mason [q. v.] he was allowed to come up to London; he stayed with Cranmer at Lambeth, and on 13 Sept. obtained a safe-conduct from the queen. Gardiner stood his friend, and found him money for his journey. He sailed for Antwerp, and reached Strasburg on 29 Oct.
Opposition to his reappointment as professor was raised by Jean Marbach (1521–1581), head of the Strasburg consistory, on the ground that he had receded from the Lutheran doctrine of the eucharist. Vermigli made a conciliatory statement of his position, but declined to subscribe the Wittenberg concordia of 1536. The senate was with him, and on 1 Jan. 1554 he was restored to his former place. In May Calvin invited him to take charge of the Italian church at Geneva, but he declined. In 1555 he gave hospitality to John Jewel [q. v.], and his house became a rallying point for a number of English exiles repelled by the internal disputes at Frankfort. Renewed opposition to his eucharistic teaching rendered his position at Strasburg untenable. An invitation from Zürich to succeed Conrad Pellican in the chair of Hebrew reached him in May 1556. He at once accepted it, and removed to Zürich in July 1556, taking Jewel with him.
At Zürich he married for the second time. He declined renewed invitations to Geneva (1557) and to Oxford (1561). With Jewel, Cox, John Parkhurst (1512?–1575) [q. v.], Edwin Sandys (1516?–1588) [q. v.], Thomas Sampson [q. v.], and others, he maintained a constant correspondence on English affairs. On the invitation of Anthony, king of Navarre, he took part in the colloquy of Poissy (9 Sept.–19 Oct. 1561), speaking in Italian to gain the ear of Catherine de Medicis. His own account of the colloquy, continued by William Stuckius, who accompanied him, is printed by Hottinger (Hist. Eccles. 1665, vii. 714 seq.). The journey was too much for him, and his health began to fail. He was seized with fever on 4 Nov., and died at Zürich on 12 Nov. 1562. A silver medal bearing his likeness was sent to his English friends. His portrait (on a panel) is in the hall of Christ Church, Oxford, and has been several times engraved.
He married, first, Catherine Dammartin (died without issue 15 Feb. 1553), described by George Abbot [q. v.] as ‘reasonably corpulent, but of most matronlike modesty,’ and skilled in cutting ‘plumstones into curious faces.’ She was buried in the cathedral at Oxford, near the tomb of St. Frideswide. In 1557 a commission against heresy, headed by James Brooks [q. v.], sought evidence of her heresy, with a view to burning her body; none was obtained, as the persons examined ‘did not understand her language.’ Cardinal Pole sent an order to Richard Martial or Marshall [q. v.], dean of Christ Church, for the disinterment of the body, as it lay near that of the saint. Martial transferred the corpse to a dungheap in his stable. In 1558 an ecclesiastical commission deputed James Calfhill [q. v.] to superintend the reinterment. The remains were identified, and, purposely mingled with supposed relics of St. Frideswide, were buried at the northeast end of the cathedral, after an oration ending ‘hic requiescit religio cum superstitione’ (see Calfhill's ‘Historia de Exhumatione’ in Hubert's Historia, 1561, 8vo). Vermigli married, secondly, Caterina Merenda, a native of Brescia, and member of the Italian church at Geneva, by whom he had two children who died in infancy, and a posthumous daughter, Maria, who married Paul Zanin. His widow married Lodovico Ronco, a merchant of Locarno.