He spent his time writing tracts on church law until he was promoted to the Dutch episcopate in 1559 by Philip II, who named him as the very first Archbishop of Utrecht (which was then confirmed in 1561 by Pope Pius IV).

By agreement between Philip II and Rome in the spirit of the Counter-Reformation, the low countries (at that time a loose set of Seventeen Provinces) received its own archbishoprics, which besides Utrecht were Mechelen and Cambrai.

These measures were not very successful, and Scheck van Toutenburg's archbishopric saw the Catholic reaction against the Council of Trent in the northern Netherlands.

Governor Margaret of Parma forced him to lead support for the decrees of the Council of Trent and led him to call a provincial synod in 1565.

The clergy and canons were fiercely opposed to the new disciplinary measures and tried to frustrate their introduction, but Schenck van Toutenburg used his power to break the opposition and to give leadership in the fight against Protestantism.

Though Hénin-Liétard was released as a term of treaty in the Pacification of Ghent in 1576, he no longer had command of Vredenburg and chose the side of William of Orange.

Schenk van Toutenburg refused to pay, and the city fathers forced the lock on his money chest to "loan" 40,000 guilders.