At the time of the Battle of Sekigahara in which Mitsunari raised armies against Ieyasu, Kiyomasa stayed in Kyushu and defeated the powers of the Western Camp in Kyushu one after another, together with Yoshitaka KURODA giving the Eastern Camp of Ieyasu support, including the schemed surrenders of Uto-jo Castle of Yukinaga and Yanagawa-jo Castle of Muneshige TACHIBANA.
慶長5年（1600年）に三成が家康に対して挙兵した関ヶ原の戦いでは九州に留まり、黒田孝高と共に家康ら東軍に協力して行長の宇土城、立花宗茂の柳川城などを開城、調略し、九州の西軍勢力を次々と破った。