After his elder brother Mototsugu died in 1591, his son Mototada NANJO succeeded the headship of Nanjo family; Motokiyo became the guardian of Mototada and assumed the works of government affairs as Utsubuki-jo Castle joban (live-in castle guardian) by residing in a residence within the castle compound.
天正19年（1591年）に元続が死去し、南条元忠が家督を継ぐと元忠の後見人になり、打吹城番として城内の屋敷に住み政務を行った。