In 1679 Ken was appointed by Charles II chaplain to the Princess Mary, wife of William of Orange. While with the court at the Hague, he incurred the displeasure of William by insisting that a promise of marriage, made to an English lady of high birth by a relative of the prince, should be kept; and he therefore gladly returned to England in 1680, when he was immediately appointed one of the king's chaplains.

He was once more residing at Winchester in 1683 when Charles came to the city with his slightly disreputable court. His residence was chosen as the home of Nell Gwynne, the King's official mistress—hardly an appropriate arrangement! But Ken stoutly objected and succeeded in making the favorite find quarters elsewhere. In August of this same year he accompanied Lord Dartmouth to Tangier as chaplain to the fleet, and Pepys, who was one of the company, has left on record some quaint and kindly reminiscences of him and of his services on board.

The fleet returned in April 1684, and a few months after, upon a vacancy occurring in the see of Bath and Wells, Ken (now Dr Ken) was appointed bishop. It is said that, upon the, occurrence of the vacancy, the King, mindful of the spirit he had shown at Winchester, exclaimed, "Where is the good little man that refused his lodging to poor Nell?" and determined that no other should be bishop. The consecration took place at Lambeth on 25 January 1685; and one of Ken's first duties was to attend the death-bed of Charles, where his wise and faithful ministrations won the admiration of everybody except Bishop Burnet.

In this year he published his Exposition on the Church Catechism, perhaps better known by its sub-title, The Practice of Divine Love.

In 1688, when James reissued his Declaration of Indulgence, Ken was one of the seven bishops who refused to publish it. He was probably influenced by two considerations: first, by his profound aversion from Roman Catholicism, to which he felt he would be giving some Episcopal recognition by compliance; but, second and more especially, by the feeling that James was compromising the spiritual freedom of the church. Along with his six brethren, Ken was committed to the Tower on 8 June 1688, on a charge of high misdemeanor; the trial, which took place on 29 June and 30 June, and which resulted in a verdict of acquittal, is a matter of history.

With the Glorious Revolution which speedily followed this impolitic trial, new troubles encountered Ken; for, having sworn allegiance to James, he thought himself thereby precluded from taking the oath to William of Orange. Accordingly, he took his place among the non-jurors, and, as he stood firm to his refusal, he was, in August 1691, superseded in his bishopric by Dr Richard Kidder, dean of Peterborough. From this time he lived mostly in retirement, finding a congenial home with Lord Weymouth, his friend from college days, at Longleat in Wiltshire; and though pressed to resume his diocese in 1703, upon the death of Bishop Kidder, he declined, partly on the ground of growing weakness, but partly no doubt from his love for the quiet life of devotion which he was able to lead at Longleat. His death took place there on 19 March 1711. and at dawn the following day, whilst his faithful friends sang "Awake, my soul, and with the sun" Bishop Ken's remains were laid to rest beneath the East Window of the Church of St. John in Frome - the nearest parish in his old Diocese of Bath and Wells. "I am dying," Ken had written, "In the Holy, Catholic and Apostolic Faith professed by the whole Church before the disunion of East and West; and, more particularly, in the Communion of the Church of England, as it stands distinguished from both Papal and Protestant innovation, and adheres to the Doctrine of the Cross." There is no finer statement of the Anglican position to be found anywhere.

He was buried at the Church of St. John the Baptist, Frome where his crypt can still be seen. He is remembered in the Church of England with a Lesser Festival on 8 June.

Little is known about Tallis's early life, but there seems to be agreement that he was born in the early 16th century, toward the close of the reign of Henry VII. His first known appointment to a musical position was as organist of Dover Priory in 1530-31, a Benedictine priory at Dover (now Dover College) in 1532. His career took him to London, then (probably in the autumn of 1538) to the Augustinian abbey of Holy Cross at Waltham until the abbey was dissolved in 1540; then he went to Canterbury Cathedral, and finally to Court as Gentleman of the Chapel Royal in 1543, composing and performing for Henry VIII during which he wrote music for the Church of England, Edward VI (1547-1553), Queen Mary (1553-1558), and Queen Elizabeth I (1558 until he died in 1585). Throughout his service to successive monarchs as organist and composer, Tallis avoided the religious controversies that raged around him, though, like William Byrd, he stayed an "unreformed Roman Catholic."

Tallis married around 1552; his wife, Joan, outlived him by four years. They apparently had no children. Late in his life he lived in Greenwich, likely close to the royal palace: a local tradition holds that he lived on Stockwell Street.
 

The earliest surviving works by Tallis, Salve intemerata virgo, Ave rosa sine spinis and Ave Dei patris filia are devotional antiphons to the Virgin Mary, which were used outside the liturgy and were cultivated in England until the fall of Cardinal Wolsey. Henry VIII's break with Roman Catholicism in 1534 and the rise of Thomas Cranmer noticeably influenced the style of music written. Texts became largely confined to the liturgy. The writing of Tallis and his contemporaries became less florid. Tallis's Mass for four voices is marked with tendencies toward a syllabic and chordal style and a diminished use of melisma. Tallis provides a rhythmic variety and differentiation of moods depending on the meaning of his texts. Tallis helped found a relationship that was specific to the combining of words and music.

The reformed Anglican liturgy was inaugurated during the short reign of Edward VI (1547-1553), and Tallis was one of the first church musicians to write anthems set to English words, although Latin continued to be used. The Catholic Mary Tudor set about undoing the religious reforms of the preceding decades. Following the accession of the Catholic Mary in 1553, the Roman Rite was restored and compositional style reverted to the elaborate writing prevalent early in the century. Two of Tallis's major works, Gaude gloriosa Dei Mater and the Christmas Mass Puer natus est nobis are believed to be from this period. Only Puer natus est nobis can be accurately dated in 1554. As was the prevailing practice, these pieces were intended to exalt the image of the Queen as well as to praise the Mother of God.

Elizabeth succeeded her half-sister in 1558, and the Act of Settlement in the following year abolished the Roman Liturgy and firmly established the Book of Common Prayer. Composers at court resumed writing English anthems, although the practice of setting Latin texts continued, growing more peripheral over time.

The mood of the country in the beginning of Elizabeth's reign leant toward the puritan, which discouraged the liturgical polyphony. Tallis wrote nine psalm chant tunes for four voices for Archbishop Parker's Psalter, published in 1567. One of the nine tunes, the "Third Mode Melody", inspired the composition of Fantasia on a Theme of Thomas Tallis by Ralph Vaughan Williams in 1910. Tallis's better-known works from the Elizabethan years include his settings of the Lamentations (of Jeremiah the Prophet)  for the Holy Week services and the unique motet Spem in alium written for eight five-voice choirs. It is thought that this 40-voice piece was part of a celebration of the Queen's 40th birthday in 1573. Tallis is mostly remembered for his role in composing office hymns and this motet, Spem in alium.