He was educated at Christ's Hospital and at Broadgate's Hall, now Pembroke College, Oxford, afterwards becoming a member of Clifford's Inn, and later of the Middle Temple.
At Oxford he lost his faith in the existence of God, but after some years, his, to his mind, miraculous escape from a near fatal accident caused him to reconsider.
Having reconciled him to the Catholic Church and assisted him in his last moments, Baker hastened to settle his own worldly affairs and to return to the cloister.
At the desire of his superiors he now devoted his time and the ample means which he had inherited, to investigating and refuting the recently started error that the ancient Benedictine congregation in England was dependent on that of Cluny, founded in 910.
At Sir Robert Cotton's, Baker came in contact with the antiquary William Camden and with other learned men of his day.
In 1624 he was sent to the newly established convent of Benedictine nuns at Cambrai (today succeeded by the community at Stanbrook Abbey) in Flanders, not as chaplain, but to aid in forming the spiritual character of the religious.
Here he remained for about nine years, during which time he wrote many of his mystical treatises, an abstract of which is contained in the work Sancta Sophia (1657) compiled by Serenus de Cressy.