On 7 March 1559 he resigned the presidency of Holy Ghost College in favour of Jean Hessels and on 22 September succeeded Michel Drieux as dean of St Peter's and vice-chancellor of the university.

The committee reported on 8 June 1565 advising that the laws on heresy should not change, but that a secret instruction be sent to the tribunals asking them to moderate punishment in accordance with the social position, sex and age of the accused, giving them leeway to sentence those convicted to hard labour, banishment or even a fine rather than to death.

At Bruges, Rythovius argued that in the interest of the public peace, King Philip should be asked to soften and mitigate the laws on heresy.

Over the subsequent months, outlaws targeted the clergy of the diocese, with the parish priests of Houtkerque, Reningelst, Hondschoote, Rexpoëde, Rubrouck and Herzeele murdered, and others mutilated or mistreated The Duke of Alva summoned Rythovius to Brussels for 4 June 1568, where he was informed that Lamoral, Count of Egmont, had been condemned to death.

The bishop pleaded for the count's life to no avail, and afterwards heard the condemned man's last confession and the next morning administered the viaticum and accompanied him to the scaffold for a final blessing.

The States of Flanders, having failed to dissuade the duke, asked the bishops of Ypres, Bruges and Ghent to petition him on their behalf.

The Pacification of Ghent of 8 November 1576 stipulated that the Catholic Faith would be maintained throughout the Low Countries with the exception of Holland and Zeeland, with a provisional suspension of the heresy laws.

In the night of 28–29 October there was a coup in which Philippe III de Croÿ, Rythovius, and the bishop of Bruges, Remi Drieux, were taken prisoner.

Aarschot was released on 10 November, but the bishops, and a number of other leading opponents of the Revolt, remained in captivity, essentially hostages, until 14 August 1581.

Rythovius was unable to return to Ypres, which remained in rebel hands until 7 April 1584, but did what he could in the towns of his diocese that had been reconquered by Alexander Farnese, such as Dunkirk and Veurne.