Although Kojima-dera Temple was involved in the disturbances of war during the Muromachi period and ebbed away, the lord of the Takatori Domain (the lord of Takatori Castle), the Honda clan, revitalized it.
室町時代には子嶋寺は戦乱に巻き込まれて衰退したが、高取藩主（高取城主）の本多氏によって再興された。