[1][2] On 3 September 1579 Wigginton was instituted to the vicarage of Sedbergh, then in Yorkshire, on the presentation of Trinity College, but found his Calvinism unpopular.
In 1581 Edwin Sandys, archbishop of York, wrote concerning Wigginton to his diocesan William Chaderton, bishop of Chester, remarking ‘He laboureth not to build, but to pull down, and by what means he can to overthrow the state ecclesiastical’ In 1584, when in London, he was appointed to preach before the judges in the church of St. Dunstan-in-the-West.
Whitgift, by then archbishop of Canterbury, sent a pursuivant to Wigginton at night while he was in bed, to forbid him to preach and require him to give a bond for his appearance at Lambeth the next day.
[2] In the following year, on the information of Edward Middleton, Whitgift gave orders to Sandys to proceed against Wigginton, and he was in consequence cited before Chaderton and deprived of his living.
[3] Later in 1586, while visiting London, he was apprehended by one of Whitgift's pursuivants, brought before the archbishop at Lambeth, and, on refusing the oath again, was committed to the White Lion prison, where he was treated harshly.
He was released before December 1588, for in that month he was again arrested in London and brought before the high commissioners at Lambeth on the charge of being concerned in the authorship of the Marprelate tracts.
[2] On 4 April 1597 he wrote to Burghley, proposing the establishment of a seminary to train men for controversy with Catholic priests, and presenting him with a manuscript anti-Catholic treatise.
He was also the author of Giles Wigginton his Catechisme (London, 1589), and of several theological treatises in manuscript that came into the possession of Dawson Turner.