In 1603 he was reconciled to Rome through the agency of Fr. Richard Lloyd, a pupil of the English College at Rome. On his homeward way, a chance meeting with Fr. William Watson involved him in suspicions of complicity in Watson's plot (the ‘Bye Plot’), but no charge was preferred, and in 1605 he joined the Benedictine community of S. Justinian at Padua, taking the religious name of ‘Augustine.’ Here he learned Italian, and made the acquaintance of his fellow-countryman Dr. Griffith, confessor to a nunnery at Milan. Obtaining leave to visit his home in 1607, he made over his Herefordshire property (Pembridge) to his nephew Henry Prichard (6 Sept.), and made several converts among his relatives and neighbours, including his sister, wife of William Parry of Llanover (himself a Catholic), who remained staunch when her husband wavered under persecution, and eventually his father, who was reconciled by Morgan Clynnog, nephew of Morys Clynnog (q.v.). Next year he was instrumental in bringing about the reconstitution of the English congregation of Benedictines. Dom Sigebert Buckley, last survivor of the pre-Reformation English Benedictines (who has been claimed as a native of Beaumaris), had got into touch with the English missioners attached to Italian congregations on their first arrival in 1603, and Baker's legal and historical knowledge were of great service in effecting their ‘aggregation’ into the restored English congregation, he himself being the first to be received into it. He was ordained priest at Reims in 1613, living meanwhile with various English Catholic families and keeping in touch with South Wales. He maintained at Douai two youths (one his nephew, who later joined the Jesuits, the other Philip Morgan, alias Powel, whom he coached in law from 1610 to 1614 and who was martyred in 1646); and recommended many Catholic children to Abergavenny grammar school, under the headship of Morgan Lewis, husband to his niece Margaret Prichard and father of David Lewis (alias Charles Baker), the last Welsh Catholic martyr (1617-1679, q.v.), keeping in touch with them and selecting one (Philip Prosser) as his special protégé. Lewis aroused Protestant suspicions, but was exonerated by the Parliament of 1626.

Gradually Baker found it wiser to cease visiting his former acquaintance when he went to Abergavenny, living in seclusion at the house of his sister Mrs. Henry Prichard except when occasionally he emerged to give free legal advice to friends or to poor people. At the very end of his life he was consulted on the proposed new charter for Abergavenny, but refused to appear publicly in the matter. In 1620 he paid his last visit to Abergavenny, taking as his companion Fr. Leander Prichard (possibly a nephew), who was afterwards his biographer. The rest of his life was spent in England and abroad. In 1624, after a short period at Douai, he became spiritual director to a community of nuns at Cambrai, remaining there till in 1633 he was recalled to Douai and vindicated by his Order from aspersions of heresy which had been cast on his works. In 1638 he returned to England. During the closing years of his life he became involved in a controversy about the autonomy of the English Benedictine congregation, in which he had the support of the Government, now under the personal rule of Charles I and eager to advance the Benedictine claims both for patriotic reasons and as a counterweight to the politically far more dangerous Jesuits. He was given access to the State papers in the Tower and the use of private libraries like that of Sir Robert Cotton (to whom he had written while still at Cambrai asking for English books for his community); and in the course of his researches he made the acquaintance of Selden, who became a ‘speciall friend,’ Camden, Spelman, and archbishop Ussher. The material he collected, put in order by his friend Fr. John (Leander) Jones (q.v.) and edited by their pupil Clement Rayner, forms an essential source for the history of the English Benedictines. He also left unfinished treatises on general ecclesiastical history and on English law, and many volumes of mystical and theological works (catalogued Cath. Rec. Soc., xxxiii), excerpts from which were published posthumously by Fr. Cressy under the title Sancta Sophia (Douai, 1657), and have often been republished. His Holy Practices also appeared in 1657, and his Secretum was published under the title Confessions by abbot McCann in 1922. These works have given him a high repute as a mystical writer. His autobiography (written 1637-8, published in Cath. Rec. Soc., xxxiii), leaves the impression of a man of simple, sincere, and lovable character, taking great delight in singing and in walking, and with a flair for conveying his religious and moral teaching in homely English or Latin rhymes, of which he made a collection in 1636, some of them remaining current in his Order as late as the 19th cent. Lives of him were written by his companion (see above) Fr. Leander Prichard (1643, repub. Cath. Rec. Soc., xxxiii), by Frs. Peter Salvin and Serenus Cressy (repub. 1932), and by abbot J. N. Sweeney (1861). He has been described as ‘a striking, if not a unique, figure in the history of post-Reformation English Catholicism’ (abbot J. McCann) and as ‘the last Welsh Catholic who played a large part in the history of Catholicism in England’ (W. Ll. Williams).