He also participated in the Polish–Muscovite War (1605–18), where he commanded the failed siege of Troitse-Sergiyeva Lavra in 1608 and later fought anti-Polish Muscovite forces near Moscow, led by Prokopy Lyapunov.

Despite an initial refusal to accept the offer of Krzysztof Mikołaj "the Thunderbolt" Radziwiłł, he took part in the Livonian War (1601–1605) and on 5 March 1603, his regiments distinguished themselves in the Battle of Rakibor, under the command of Jan Karol Chodkiewicz.

The regiment commanded by Sapieha miraculously endured one of the main counter-attacks of the Swedish army, led personally by King Charles IX of Sweden.

From January to March 1611 he led the negotiations with the boyars and hoped to either weaken the position of the king's troops favoured, supported and personally commanded by the great Hetman Stanisław Żółkiewski, or place himself on the Russian throne.

Demoralized by the lack of paid salaries and of poor hygienic conditions in the camps, the Polish soldiers fell into mental apathy and immediately stopped fighting.

Polish actor Michał Żebrowski portrayed Hetman Kybowsky (character loosely based on Jan Piotr Sapieha) in the 2007 Russian historical film 1612.