After the failed rebellion, he sponsored the creation of the Roman Catholic monastery of Kalwaria Zebrzydowska, which is regarded as one of the most important pilgrimage sites of Poland.

In 1595, Zebrzydowski participated in Jan Zamoyski's raid to Moldova, and in 1601, was promoted to the title of Voivode of Kraków.

He stated that in order to restrain the King and control the Sejm, the nobility had to gather near Warsaw, adding that the homeland was in danger.

His speech was warmly welcomed, and on 23 February, the sejmik of Lesser Poland, which took place in Nowy Korczyn, rejected royal plans, urging the Polish–Lithuanian nobility to concentrate at Stężyca, on 9 April.

Since the rebellious nobility, gathered at Stężyca, had no idea how to fight the King, another meeting was called in Lublin, on 5 June.

On 14 February 1607, local nobility gathered at a sejmik in Koło urged their Lesser Polish brethren to complete the rebellion, and to meet on 28 March in Jędrzejów.

By that time, however, the rokosz lost its momentum, and the rebel camp was first moved to Wąchock, then to Sieciechów, and finally to Czersk.

He did not fight in the Polish–Muscovite War (1605–18), instead sending a few hundred of soldiers to guard the Transilvanian border against the possible invasion of Gabriel Bathory.