In May 1567, he attended on the Lord Deputy of Ireland, Sir Henry Sidney, at Drogheda, where he agreed to conform to the reformed faith and to hold his See from the Crown.

He complained that Cashel was only worth £98 and – in spite of the misgivings of William Cecil, Lord Burghley – was granted the See of Waterford and Lismore in commendam, which he held until 1589, and then again from 1592 upon the death of Bishop Wetherhead.

However, Magrath continued to court favour with the authorities, and in 1584 he did arrest the Catholic Bishop of Emly, Maurice MacBrien, who died two years later in custody in Dublin Castle.

During his visit he sought to convert to Protestantism the condemned Gaelic Prince of Breifne, Brian O'Rourke, who scorned the bishop at the foot of the gallows-ladder before his execution in London.

At about this time Magrath's cousin, Dermot Creagh, was the Catholic Bishop of Cork and Cloyne with Legatine authority in Munster, and they remained on mutual terms.

Magrath appears to have feared that his soul was in jeopardy, and with a view to repentance and reconciliation with Rome, took care that his cousin would not be captured, while at the same time feeding information to the Crown about his whereabouts.

In 1596, during the Nine Years War, Archbishop Magrath and the 10th Earl of Ormond were involved in a conference at Faughart with the Northern chiefs, offering them the possession of Ulster, apart from County Louth, Carrickfergus and Newry as these areas were held by English garrisons.

He claimed poverty owing to the war, but Cecil soon complained that he was allowing the Anglican Church of Ireland to lie like "an hogsty" and sought Sir George Carew to remonstrate with him over this neglect.

He was ultimately compelled to accept the Sees of Killala and Achonry in Connacht, which were of little worth: in 1610, he complained he had not received their possession, and the full grant was not made until 1611.

The Lord Deputy, Sir Arthur Chichester, had a poor opinion of Magrath, describing him as "stout and wilful", but held back for fear of his influence amongst the Ulster Irish, and Stafford too spoke of his oppressions.

In 1612, the underground Irish Provincial of the Franciscan Order still held out hope of Magrath's reconciliation with Rome; in 1617 it was thought he might exchange the Rock of Cashel for the Capitoline, where he had spent his youth.

On the Protestant side, he is widely blamed for the rapacious financial corruptions which gave the Reformation in Ireland a black eye from which it has never recovered.

Magrath married a Roman Catholic, Áine Ni Meara, daughter of John O'Meara of Lisany, in County Tipperary; and had issue, Turlough, Redmond, James, Brian, Marcus, Mary, Cicely, Anne, and Ellis.