He then changed his opinions, and after a sermon in a puritan vein in Great St. Mary's by John Millen or Milayn, a fellow of Christ's, in October 1573, he controverted its teaching in the same place during the afternoon.
When John Whitgift resigned the mastership of Trinity in June 1577, on his election to the see of Worcester, he strongly recommended Howland, a personal friend, to Burghley, as his successor.
In 1578 he served the office of vice-chancellor, in which capacity he, at the head of the university, waited on the queen on her visit to Audley End, on 27 July 1578, and presented her with a Greek Testament and a pair of gloves, making a suitable oration.
The choice of a successor threatened to involve the college in a fierce internal struggle and it was arranged that Howland should continue to hold the mastership with his bishopric; he resigned in February 1586.
On the death of Archbishop John Piers in 1594, Howland was earnestly recommended for the see of York by the lord president Henry Hastings, 3rd Earl of Huntingdon, and the council of the north; Matthew Hutton was appointed.
The deprivation of Robert Cawdrey, vicar of South Luffenham, Rutland, led to a long dispute.