During the 1587 free royal election, he supported Sigismund Vasa, and financially supported Vasa's faction in the War of the Polish Succession (1587–88). After the conflict, he was named Voivode of Lublin and court hetman. In 1595, Zebrzydowski participated in Jan Zamoyski's raid to Moldova, and in 1601, was promoted to the title of Voivode of Kraków. In ca. 1605, he became dissatisfied with King Zygmunt's attempts to strengthen royal power and weaken the nobility. The King tried to reform the administration and the treasury, also to create a permanent army. Zebrzydowski opposed it, as in his opinion, royal plans were a threat to the so-called Golden Liberty.
