During the Time of Troubles, he participated in the struggle against the supporters of False Dmitry II and Polish invaders. In 1607, Khovansky was sent to Mikhailov, which had been occupied by the opponents of Vasili IV of Russia, but his attacks on this city were rebuffed. 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. Khovansky managed to rendezvous with the Swedes near Staritsa, capture Rzhev, and beset Bely. 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.