In the past, it had been said that he fought in the Battle of Sekigahara (1600) for the Western army (the Toyotomi forces), because the Shinmen clan, which Muni SHINMEN (Musashi's father) had served once, fought under Hideie UKITA of the Western army; however, according to "Kuroda-han Bugencho" (The Register of the Kuroda Clan), since before the battle, Muni had served the Kuroda family which had governed Buzen Province (the information is found in the article of 1602 and 1604 of the register), therefore, presumably, in the battle Muni and Musashi fought for the Eastern army (the Tokugawa forces) following Yoshitaka KURODA (Josui KURODA) in Kyushu region.
慶長5年（1600年）の関ヶ原の戦いでは従来、父無二の旧主君であった新免氏が宇喜多秀家配下であったことからそれに従って西軍に参加したと言われてきたが、父の新免無二が関ヶ原の戦い以前に東軍の黒田家に仕官していたことを証明する黒田家の文書（『慶長7年・同9年黒田藩分限帖』）が存在することから、父と共に当時豊前を領していた黒田孝高に従い東軍として九州で戦った可能性が高い。