The 1560s were also important formative years for Byrd the Composer. His Short Service, an unpretentious setting of items for the Anglican Matins, Communion and Evensong services, which seems to have been designed to comply with the Protestant reformers’ demand for clear words and simple musical textures, may well have been composed during the Lincoln years. It is at any rate clear that Byrd was composing Anglican church music, for when he left Lincoln the Dean and Chapter continued to pay him at a reduced rate on condition that he would send the cathedral his compositions. Byrd had also taken serious strides with instrumental music. The seven In Nomine settings for consort (two a4 and five a5), at least one of the consort fantasias (Neighbour F1 a6) and a number of important keyboard works were apparently composed during the Lincoln years. The latter include the Ground in Gamut (described as "Mr Byrd's old ground") by his Future pupil Thomas Tomkins, the A minor Fantasia, and probably the first of Byrd's great series of keyboard pavanes and galliards, a composition which was transcribed by Byrd from an original for five-part consort. All these show Byrd gradually emerging as a major figure on the Elizabethan musical landscape.

Byrd's first known professional employment was his appointment in 1563 as organist and master of the choristers at Lincoln Cathedral. Residing at what is now 6 Minster Yard Lincoln, he remained in post until 1572. His period at Lincoln was not entirely trouble-free, for on 19 November 1569 the Dean and Chapter cited him for 'certain matters alleged against him' as the result of which his salary was suspended. Since Puritanism was influential at Lincoln, it is possible that the allegations were connected with over-elaborate choral polyphony or organ playing. A second directive, dated 29 November, issued detailed instructions regarding Byrd's use of the organ in the liturgy. On 14 September 1568, Byrd married Julian Birley; it was a long-lasting and fruitful union which produced at least seven children.

From the early 1570s onwards Byrd became increasingly involved with Catholicism, which, as the scholarship of the last half-century has demonstrated, became a major factor in his personal and creative life. As John Harley has shown, it is probable that Byrd's parental family were Protestants, though whether by deeply felt conviction or nominal conformism is not clear. Byrd himself may have held Protestant beliefs in his youth, for a recently discovered fragment of a setting of an English translation of Martin Luther's hymn "Erhalt uns, Herr, bei deinem Wort", which bears an attribution to "Birde" includes the line "From Turk and Pope defend us Lord". However, from the 1570s onwards he is found associating with known Catholics, including Lord Thomas Paget, to whom he wrote a petitionary letter on behalf of an unnamed friend in about 1573. Byrd's wife Julian was first cited for recusancy (refusing to attend Anglican services) at Harlington in Middlesex, where the family now lived, in 1577. Byrd himself appears in the recusancy lists from 1584.

Byrd obtained the prestigious post of Gentleman of the Chapel Royal in 1572 following the death of Robert Parsons, a gifted Composer who drowned in the Trent near Newark on 25 January of that year. Almost from the outset Byrd is named as 'organist', which however was not a designated post but an occupation for any Chapel Royal member capable of filling it. This career move vastly increased Byrd's opportunities to widen his scope as a Composer and also to make contacts at Court. Queen Elizabeth (1558–1603) was a moderate Protestant who eschewed the more extreme forms of Puritanism and retained a fondness for elaborate ritual, besides being a music lover and keyboard player herself. Byrd's output of Anglican church music (defined in the strictest sense as sacred music designed for performance in church) is surprisingly small, but it stretches the limits of elaboration then regarded as acceptable by some reforming Protestants who regarded highly wrought music as a distraction from the Word of God.

Byrd enjoyed a high reputation among English Musicians. As early as 1575 Richard Mulcaster and Ferdinand Haybourne praised Byrd, together with Tallis, in poems published in the Tallis/Byrd Cantiones. Despite the financial failure of the publication, some of his other collections sold well, while Elizabethan scribes such as the Oxford academic Robert Dow, the Windsor lay clerk John Baldwin, and a school of scribes working for the Norfolk country gentleman Sir Edward Paston copied his music extensively. Dow included Latin distichs and quotations in praise of Byrd in his manuscript collection of music, the Dow Partbooks (GB Och 984-988), while Baldwin included a long doggerel poem in his Commonplace Book (GB Lbm Roy App 24 d 2) ranking Byrd at the head of the Musicians of his day:

The Cantiones were a financial failure. In 1577 Byrd and Tallis were forced to petition Queen Elizabeth for financial help, pleading that the publication had "fallen oute to oure greate losse" and that Tallis was now "verie aged". They were subsequently granted the leasehold on various lands in East Anglia and the West Country for a period of 21 years.

His involvement with Catholicism took on a new dimension in the 1580s. Following Pope Pius V's papal bull Regnans in Excelsis, in 1570, which absolved Elizabeth's subjects from allegiance to her and effectively made her an outlaw in the eyes of the Catholic Church, Catholicism became increasingly identified with sedition in the eyes of the Tudor authorities. With the influx of missionary Priests trained at the English College, Douai, (now in France but then part of the Spanish Netherlands) and in Rome from the 1570s onwards, relations between the authorities and the Catholic community took a further turn for the worse. Byrd himself is found in the company of prominent Catholics. In 1583 he got into serious trouble because of his association with Paget, who was suspected of involvement in the Throckmorton Plot, and for sending money to Catholics abroad. As a result of this, Byrd's membership of the Chapel Royal was apparently suspended for a time, restrictions were placed on his movements, and his house was placed on the search list. In 1586 he attended a gathering at a country house in the company of Father Henry Garnett (later executed for complicity in the Gunpowder Plot) and the Catholic poet Robert Southwell.

Byrd's acquaintance with the Petre family extended back at least to 1581 (as his surviving autograph letter of that year shows) and he spent two weeks at the Petre household over Christmas in 1589. He was ideally equipped to provide elaborate polyphony to adorn the music making at the Catholic country houses of the time. The continued adherence of Byrd and his family to Catholicism continued to cause him difficulties, though a surviving reference to a lost petition apparently written by Byrd to Robert Cecil, Earl of Salisbury sometime between 1605 and 1612 suggests that he had been allowed to practise his religion under licence during the reign of Elizabeth. Nevertheless, he regularly appeared in the quarterly local assizes and was reported to the archdeaconry court for non-attendance at the parish church. He was required to pay heavy fines for recusancy. No doubt his wide circle of friends and patrons among the nobility and gentry were able to ensure that he escaped more severe penalties.

Byrd's output of about 470 compositions amply justifies his reputation as one of the great masters of European Renaissance music. Perhaps his most impressive achievement as a Composer was his ability to transform so many of the main musical forms of his day and stamp them with his own identity. Having grown up in an age in which Latin polyphony was largely confined to liturgical items for the Sarum rite, he assimilated and mastered the Continental motet form of his day, employing a highly personal synthesis of English and continental Models. He virtually created the Tudor consort and keyboard fantasia, having only the most primitive Models to follow. He also raised the consort song, the church anthem and the Anglican Service setting to new heights. Finally, despite a general aversion to the madrigal, he succeeded in cultivating secular vocal music in an impressive variety of forms in his three sets of 1588, 1589 and 1611.

All three Mass cycles employ other early Tudor features, notably the mosaic of semichoir sections alternating with full sections in the four-part and five-part Masses, the use of a semichoir section to open the Gloria, Credo, and Agnus Dei, and the head-motif which links the openings of all the movements of a cycle. However, all three cycles also include Kyries, a rare feature in Sarum Rite mass settings, which usually omitted it because of the use of tropes on festal occasions in the Sarum Rite. The Kyrie of the three-part Mass is set in a simple litany-like style, but the other Kyrie settings employ dense imitative polyphony. A special feature of the four-part and five-part Masses is Byrd's treatment of the Agnus Dei, which employ the technique which Byrd had previously applied to the petitionary clauses from the motets of the 1589 and 1591 Cantiones sacrae. The final words dona nobis pacem ("grant us peace"), which are set to chains of anguished suspensions in the Four-Part Mass and expressive block homophony in the five-part setting, almost certainly reflect the aspirations of the troubled Catholic community of the 1590s.

The greater part of the two collections consists of settings of the Proprium Missae for the major feasts of the church calendar, thus supplementing the Mass Ordinary cycles which Byrd had published in the 1590s. Normally, Byrd includes the Introit, the Gradual, the Alleluia (or Tract in Lent if needed), the Offertory and Communion. The feasts covered include the major feasts of the Virgin Mary (including the votive masses for the Virgin for the four seasons of the church year), All Saints and Corpus Christi (1605) followed by the feasts of the Temporale (Christmas, Epiphany, Easter, Ascension, Whitsun, and Feast of Saints Peter and Paul (with additional items for St Peter's Chains and the Votive Mass of the Blessed Sacrament) in 1607. The verse of the Introit is normally set as a semichoir section, returning to full choir scoring for the Gloria Patri. Similar treatment applies to the Gradual verse, which is normally attached to the opening Alleluia to form a single item. The liturgy requires repeated settings of the word "Alleluia", and Byrd provides a wide variety of different settings forming brilliantly conceived miniature fantasias which are one of the most striking features of the two sets. The Alleluia verse, together with the closing Alleluia, normally form an item in themselves, while the Offertory and the Communion are set as they stand.

The period up to 1591 also saw important additions to Byrd's output of consort music, some of which have probably been lost. Two magnificent large-scale compositions are the Browning, a set of 20 variations on a popular melody (also known as "The leaves be green") which evidently originated as a celebration of the ripening of nuts in autumn, and an elaborate ground on the formula known as the Goodnight Ground. The smaller-scale fantasias (those a3 and a4) use a light-textured imitative style which owes something to Continental Models, while the five and six-part fantasias employ large-scale cumulative construction and allusions to snatches of popular songs. A good Example of the last type is the Fantasia a6 (No 2) which begins with a sober imitative paragraph before progressively more fragmented textures (working in a quotation from Greensleeves at one point). It even includes a complete three-strain galliard, followed by an expansive coda (for a performance on YouTube, see under 'External links' below). The single five-part fantasia, which is apparently an early work, includes a canon at the upper fourth.

It was evidently at the behest of this circle of friends that Byrd now embarked on a grandiose programme to provide a cycle of liturgical music covering all the principal feasts of the Catholic Church calendar. The first stage in this undertaking comprised the three Ordinary of the Mass cycles (in four, three and five parts), which were published by Thomas East between 1592 and 1595. The editions are undated (dates can be established only by close bibliographic analysis) do not name the printer and consist of only one bifolium per partbook to aid concealment, reminders that the possession of heterodox books was still highly dangerous. All three works contain retrospective features harking back to the earlier Tudor tradition of Mass settings which had lapsed after 1558, along with others which reflect Continental influence and the liturgical practices of the foreign-trained incoming missionary Priests. Mass for Four Voices, or the Four-Part Mass, which according to Joseph Kerman was probably the first to be composed, is partly modelled on John Taverner's Mean Mass, a highly regarded early Tudor setting which Byrd would probably have sung as a choirboy. Taverner's influence is particularly clear in the scale figures rising successively through a fifth, a sixth and a seventh in Byrd's setting of the Sanctus.

In about 1594 Byrd's career entered a new phase. He was now in his early fifties, and seems to have gone into semi-retirement from the Chapel Royal. He moved with his family from Harlington to Stondon Massey, a small village near Chipping Ongar in Essex. His ownership of Stondon Place, where he lived for the rest of his life, was bitterly contested by Joanna Shelley, with whom he engaged in a protracted and unedifying legal dispute lasting about a decade and a half. The main reason for the move was apparently the proximity of Byrd's patron Sir John Petre (the son of the former Secretary of State Sir william Petre). A wealthy local landowner, Petre was a discreet Catholic who maintained two local manor houses, Ingatestone Hall and Thorndon Hall, the first of which still survives in a much-altered state (the latter has been rebuilt). Petre held clandestine Mass celebrations, with music provided by his servants, which were subject to the unwelcome attention of spies and paid informers working for the Crown.

In 1597 Byrd's pupil Thomas Morley dedicated his treatise A Plaine and Easie Introduction to Practicall Musicke to Byrd in flattering terms, though he may have intended to counterbalance this in the main text by some sharply satirical references to a mysterious "Master Bold". In The Compleat Gentleman (1622) Henry Peacham (1576–1643) praised Byrd in lavish terms as a Composer of sacred music:

Finally, and most intriguingly, it has been suggested that a reference to "the bird of loudest lay" in Shakespeare's mysterious allegorical poem The Phoenix and the Turtle may be to the Composer. The poem as a whole has been interpreted as an elegy for the Catholic martyr St Anne Line, who was executed at Tyburn on 27 February 1601 for harbouring Priests.

The 1605 set also contains a number of Miscellaneous items which fall outside the liturgical scheme of the main body of the set. As Philip Brett has pointed out, most of the items from the four- and three-part sections were taken from the Primer (the English name for the Book of hours), thus falling within the sphere of private devotions rather than public worship. These include, inter alia, settings of the four Marian antiphons from the Roman Rite, four Marian hymns set a3, a version of the Litany, the gem-like setting of the Eucharistic hymn Ave verum Corpus, and the Turbarum voces from the St John Passion, as well as a series of Miscellaneous items.

In stylistic terms the motets of the Gradualia form a sharp contrast to those of the Cantiones sacrae publications. The vast majority are shorter, with the discursive imitative paragraphs of the earlier motets giving place to double phrases in which the counterpoint, though intricate and concentrated, assumes a secondary level of importance. Long imitative paragraphs are the exception, often kept for final climactic sections in the minority of extended motets. The melodic writing often breaks into quaver (eighth-note) motion, tending to undermine the minim (half-note) pulse with surface detail. Some of the more festive items, especially in the 1607 set, feature vivid madrigalesque word-painting. The Marian hymns from the 1605 Gradualia are set in a light line-by-line imitative counterpoint with crotchet pulse which recalls the three-part English songs from Songs of sundrie natures (1589). For obvious reasons, the Gradualia never achieved the popularity of Byrd's earlier works. The 1607 set omits several texts, which were evidently too sensitive for publication in the light of the renewed anti-Catholic persecution which followed the failure of the Gunpowder Plot in 1605. A contemporary account which sheds light on the circulation of the music between Catholic country houses, refers to the arrest of a young Frenchman named Charles de Ligny, who was followed from an unidentified country house by spies, apprehended, searched and found to be carrying a copy of the 1605 set. Nevertheless, Byrd felt safe enough to reissue both sets with new title pages in 1610.

Byrd's last collection of English songs was Psalms, Songs and Sonnets, published in 1611 (when Byrd was over 70) and dedicated to Francis Clifford, 4th Earl of Cumberland, who later also received the dedication of Thomas Campion's First Book of Songs in about 1613. The layout of the set broadly follows the pattern of Byrd's 1589 set, being laid out in sections for three, four, five and six parts like its predecessor and embracing an even wider miscellany of styles (perhaps reflecting the influence of another Jacobean publication, Michael East's Third Set of Books (1610). Byrd's set includes two consort fantasias (a4 and a6) as well as eleven English motets, most of them setting prose texts from the Bible. These include some of his most famous compositions, notably Praise our Lord, all ye Gentiles (a6) This day Christ was born (a6) and Have mercy upon me (a6) which employs alternating phrases with verse and full scoring and also circulated as a church anthem. There are more carols set in verse and burden form as in the 1589 set as well as lighter three and four-part songs in Byrd's "sonnets and pastorals" style. Some items are, however, more tinged with madrigalian influence than their counterparts in the earlier set, making clear that the short-lived madrigal vogue of the 1590s had not completely passed Byrd by. Many of the songs follow, and develop further, types already established in the 1589 collection.

Byrd also contributed eight keyboard pieces to Parthenia (winter 1612–13), a collection of 21 keyboard pieces engraved by william Hole, and containing music by Byrd, John Bull and Orlando Gibbons. It was issued in celebration of the forthcoming marriage of James I's daughter Princess Elizabeth to Frederick V, Elector Palatine, which took place on 14 February 1613. The three composers are nicely differentiated by seniority, with Byrd, Bull and Gibbons represented respectively by eight, seven and six items. Byrd's contribution includes the famous Earl of Salisbury Pavan, composed in memory of Robert Cecil, 1st Earl of Salisbury, who had died on 24 May 1612, and its two accompanying galliards. Byrd's last published compositions are four English anthems printed in Sir william Leighton's Teares or Lamentacions of a Sorrowfull Soule (1614).

Thanks largely to the research of John Harley, knowledge of Byrd's biography has expanded in recent years. According to Harley, Thomas Byrd, the grandson of Richard Byrd of Ingatestone, Essex, probably moved to London in the 15th century. Thereafter succeeding generations of the family are described as gentlemen. william Byrd was born in London, the son of another Thomas Byrd about whom nothing further is known, and his wife, Margery. The specific year of Byrd's birth is uncertain. In his will, dated 15 November 1622, he describes himself as "in the 80th year of my age", suggesting a birthdate of 1542 or 1543. However a document dated 2 October 1598 written in his own hand states that he is "58 yeares or ther abouts", indicating an earlier birthdate of 1539 or 1540. Byrd had two brothers, Symond and John, who became London merchants, and four sisters, Alice, Barbara, Mary, and Martha.

Byrd was an active and influential Teacher. As well as Morley, his pupils included, Peter Philips, Thomas Tomkins and probably Thomas Weelkes, the first two of whom were important contributors to the Elizabethan and Jacobean virginalist school. However, by the time Byrd died in 1623 the English musical landscape was undergoing profound changes. The principal virginalist composers died off in the 1620s (except for Giles Farnaby, who died in 1640, and Thomas Tomkins, who lived on until 1656) and found no real successors. Thomas Morley, Byrd's other major composing pupil, devoted himself to the cultivation of the madrigal, a form in which Byrd himself took little interest. The native tradition of Latin music which Byrd had done so much to keep alive more or less died with him, while consort music underwent a huge change of character at the hands of a brilliant new generation of professional Musicians at the Jacobean and Caroline courts. The Civil War, and the change of taste brought about by the Restoration, created a cultural hiatus which adversely affected the cultivation of Byrd's music together with that of Tudor composers in general. In a small way, it was his Anglican church music which came closest to establishing a continuous tradition, at least in the sense that some of it continued to be performed in choral foundations after the Restoration and into the eighteenth century. Byrd's exceptionally long lifespan meant that he lived into an age in which many of the forms of vocal and instrumental music which he had made his own were beginning to lose their appeal to most Musicians. Despite the efforts of eighteenth- and nineteenth-century antiquarians, the Reversal of this judgement had to wait for the pioneering work of twentieth-century scholars from E. H. Fellowes onwards. In more recent times Joseph Kerman, Oliver Neighbour, Philip Brett, John Harley, Richard Turbet, Alan Brown, Kerry McCarthy, and others have made major contributions to increasing our understanding of Byrd's life and music. In 1999, Davitt Moroney's recording of Byrd's complete keyboard music was released on Hyperion (CDA66551/7; re-issued as CDS44461/7). This recording, which won the 2000 Gramophone Award in the Early Music category and a 2000 Jahrespreis der deutschen Schallplattenkritik, came with a 100-page essay by Moroney on Byrd's keyboard music. In 2010, The Cardinall's Musick under the direction of Andrew Carwood completed their recorded survey of Byrd's Latin church music. This series of thirteen recordings is the first time that all Byrd's Latin music is available on disc.

During his later years Byrd also added to his output of consort songs, a number of which were discovered by Philip Brett and Thurston Dart in Harvard in 1961. They probably reflect Byrd's relationship with the Norfolk landowner and music-lover Sir Edward Paston (1550–1630) who may have written some of the poems. The songs include elegies for public figures such as the Earl of Essex (1601) and Henry Prince of Wales (1612). Others refer to local notabilities or incidents from the Norfolk area.

Some sets of keyboard variations, such as The Hunt's Up and the imperfectly preserved set on Gypsies’ Round also seem to be early works. As we have seen, Byrd had begun setting Latin liturgical texts as a teenager, and he seems to have continued to do so at Lincoln. Two exceptional large-scale psalm motets, Ad Dominum cum tribularer (a8) and Domine quis habitabit (a9), are Byrd's contribution to a paraliturgicall form cultivated by Robert White and Robert Parsons. De lamentatione, another early work, is a contribution to the Elizabethan practice of setting groups of verses from the Lamentations of Jeremiah, following the format of the Tenebrae lessons sung in the Catholic rite during the last three days of Holy Week. Other contributors in this form include Tallis, White, Parsley and the elder Ferrabosco. It is likely that this practice was an expression of Elizabethan Catholic nostalgia, as a number of the texts suggest.