His antipathy for the Catholic League, shared by his brother Président Christophe de Thou, made his position difficult when the people of Chartres, who were devoted to the League, shut their gates to the troops of King Henry III on 17 January 1589 and subsequently welcomed Charles of Lorraine, Duke of Mayenne, recognizing the aged Cardinal de Bourbon as king.

On 21 September 1591 he attended the assembly of bishops, which declared "null, unjust and suggested by the malice of the enemies of France Pope Gregory XIV's Bull of Excommunication against Henry of Navarre, and on 25 July 1593 he assisted at Henry IV's abjuration in St.-Denis.

Instead of the Sainte Ampoule there was brought from Tours a miraculous oil preserved in Marmoutier Abbey.

The anointing took place on 27 February 1594, and the next day Nicolas de Thou bestowed on the king the Collar of the Order of the Holy Ghost.

He left various pastoral writings and a book entitled Cérémonies observées au sacre et couronnement d'Henri IV, roi de France.