During the Time of Troubles, he participated in the struggle against the supporters of False Dmitry II and Polish invaders.
In 1608, he and Prokopy Lyapunov fought against the Polish army in the Ryazan region, but was defeated by Aleksander Józef Lisowski at Zaraysk.
In 1610, Khovansky fought alongside Prince Mikhail Skopin-Shuisky, who ordered him to combine forces with the Swedish army, occupy the southern part of the Tver region, and prevent the enemy from regrouping.
Hetman Stanisław Żółkiewski was dispatched to aid the Polish army, but Khovansky avoided the collision and moved towards Mozhaysk in order to combine forces with Dmitry Shuisky.
In Spring 1615, he was granted the title of boyar and sent to the outskirts of Smolensk to command the inactive Russian army.