He was minister-favourite of King and Emperor Matthias (1609-1618) and a leading advocate for peace between the empire's different confessional leagues before the Thirty Years' War.

Emperor Rudolf II then became aware of him as a promising candidate for the priesthood and wanted to use him for his plans for a campaign against his Protestant noble estates and towns, as well as for a church reform in Lower Austria.

[2] The emperor and his advisors pressured the prince-bishop of Passau, Urban of Trenbach, to make Klesl his official representative in Vienna to carry out a reform of the Catholic clergy.

As cathedral provost and chancellor of the university, he worked on behalf of the emperor to make adherence to the Catholic confession a duty for professors and students.

Klesl’s moderate measures during his campaign to Catholicise Lower Austria again became the source of some tension with Jesuits like the hardliner Father Georg Scherer, which soon led to an open contention.

Unverzagt proposed making Klesl bishop of the small rundown Bishopric of Vienna, which was intended to take the wind out of his sails.

[4] In 1598, Archduke Maximilian III, who presided over the Hungarian Diet in Pressburg for his brother Matthias, announced Klesl’s nomination as Bishop of Vienna.

Klesel tried to thread a marriage of Matthias to Bavarian Princess Magdalena to get the Dukes of Bavaria as Catholic allies in the struggle for the throne of Rudolf II.

Klesl opposed the policy, but the final decision lay in the hands of the council around Matthias and, increasingly, Karl I von Liechtenstein, privy councillor of Rudolf II and sometimes his high steward.

In spring 1609, Klesl finally reached the high point of his power in Vienna by becoming the minister-favourite of Matthias, but to be formally the president of privy council, he had to wait until January 1613.

The ecclesiastical (bishop) electors supported Archduke Albrecht VII, the brother of Matthias and the ruler of the Spanish Netherlands, to be the next emperor.

Maximilian III saw that as a tactic to prolong the election and so Klesl needed protection against his enemies in the House of Austria and its Catholic supporters.

Klesl received Santa Maria degli Angeli as his titular church but in 1623 switched to San Silvestro in Capite.

The uprising in Bohemia after the Defenestration if Prague ultimately led to the beginning of the Thirty Years' War and had brought about the end of Klesl’s position as minister-favourite because of his preferential treatment of a moderate reaction since the emperor lacked the money for a military answer, and Philip III signalled no strong assistance.

By papal diplomacy, especially by Cardinal Ludovico Ludovisi, Klesl could be transferred to Castel Sant’ Angelo, in Rome, on 23 October 1622 and the accusations against him were so reduced that no legitimate reason for his arrest remained.

In Rome, Klesl carried on political activities in support for his earlier enemies Maximilian I of Bavaria and Johann Schweikhart von Cronberg, Elector of Mainz.