Nothing is known of Merbecke's musical training, although he seems to have flourished in collegiate life during his youth. By 1531 he was a member of St George's Chapel, Windsor, when his name heads the list of singing-men, and from 1541 he served as chapel organist. At this time the Protestant movement was strong in Europe, and much underground thought and literature was being trafficked into England for enthusiasts and would-be converts. Merbecke was certainly among this company, even whilst serving in the king's royal chapel at Windsor. In 1543, however, his double-life was revealed and, with two of his colleagues at St George's, Merbecke was arrested for heresy and condemned to death at the stake. The composer was accused of keeping and writing heretical documents (at this time he near completed a concordance of the English Bible, and authored a number of studies on Calvinism), and expressing disdain for the Catholic Mass. However, with the intervention of Stephen Gardiner, Bishop of Winchester, and others, Merbecke was reprieved by Henry VIII. Upon his release in 1545 he returned to his post at Windsor where, once the political climate had cooled, he happily remained to the end of his days. He died at a presumably ripe age in 1585, when John Mundy succeeded him as organist of St George's.
John Merbecke is today best remembered as the composer of the Booke of Common Praier Noted, published in 1550. This was an offering to the newly reformed English church of simple musical settings for the 1549 Prayer Book, based on traditional plainsong melodies but adapted to the vernacular. Merbecke's tunes are still sung today in several Anglican, Methodist, and other Protestant churches throughout the world. Few who sing his melodies are aware, however, that before the English Reformation Merbecke was a highly skilled composer for the Latin church.
By the mid 1540s high Catholic ritual and the Latin mysteries were shunned in England, and a new religion accessible to all was beginning to take form. This change affected virtually every aspect of religious life and art, and music became one of the principal casualties. The elaborate polyphonic style of English composition exemplified by the Eton, Caius and Lambeth choirbooks was no longer accepted and a simpler, more direct form of musical expression was required. Composers for the old Latin rite adapted to these changes in different ways: Tallis and Sheppard moved with the times and led a wave in the production of simple but effective settings of English anthems and services, while staunch Catholics like Nicholas Ludford seem to have abandoned composition altogether (or at least until the brief Latin revival under Mary). The career of John Merbecke took a somewhat more radical turn.
Merbecke's extant polyphonic output amounts to only four works. Missa Per arma iustitie uniquely survives in the Forrest-Heyther partbooks. The Marian text Ave Dei patris filia is to be found in the Peterhouse partbooks. The Jesus antiphon Domine Ihesu Christe, arguably the most successful of his surviving compositions, is an altogether more substantial and structurally coherent work, which at many points appears to mirror his progressive religious beliefs, is to be found in John Sadler's partbook from c. 1585. A Virgin and Mother was probably adapted by John Baldwin, who copied the manuscript (in the early 17th Century) in which it singularly survives.
Merbecke's Mass Per arma justitiae (on the antiphon at Terce in the first week of Lent) and his antiphons Ave Dei Patris filia and Domine Jesu Christe,in the Forrest-Heyther partbooks, are competent and craftsmanlike, but of little positive interest. In the Preface to his Biblical Concordance, written in 1550 some years after his conversion to Calvinism, Merbecke clearly repudiated works such as these, saying that 'in the study of music and playing on organs ... I consumed vainly the greatest part of My life'; his Book of Common Prayer Noted of the same year, with its simple Communion setting which has made Merbecke's name so very widely known, was not so much composition as the arrangement of plainsong melodies to the words of the new English liturgy.