However, during the Edo period, Todai-ji Temple declined even further since the bakufu deprived the Temple of its manors, and the Temple was not integrated into the bakufu system of governance using temples, subsequently in the Meiji period, Tonan-in Temple, an influential branch temple (in Nara City) was ruined.
しかし、江戸時代にはいって、荘園が取上げられ寺請制度の一翼を担わなかったこともあって、衰退がすすみ、明治時代にはいると大きな勢力を誇っていた子院の東南院(奈良市)も滅んだ。