In 1867, all Shinsengumi members including Kondo were recruited as shogunate retainers, but in October of the same year, Shusuke died of disease at the temporary residence in Nijukki-cho, Ushigome.
慶応3年（1867年）、近藤はじめ新選組全員が幕臣取り立てとなったその年の10月、移転したばかりの牛込廿騎組屋敷の寓居にて病死した。