In the Heian Period, Todai-ji was affected by the Emperor Kanmu's Nanto Buddhism Oppression Plan, and due to the plan the Office of Todai-ji Temple Construction was abolished, and there were incidents such as the Kodo Hall and Sanmen Sobo (priests and monks dormitories constructed to the north, east and west of the Kodo Hall) being burnt from an accidental fire, the Saito (Western Tower) being hit by lightening, and the Nandai-mon Gate and the Shoro (Bell Tower) being broken in a storm; but later on, from reverence, the Imperial family and nobility donated private estates including the Kuroda-no-sho and Todai-ji Temple developed them.
また、平安時代に入ると、桓武天皇の南都仏教抑圧策により「造東大寺所」が廃止されるなどの圧迫を受け、また講堂と三面僧房が失火で、西塔が落雷で焼失したり、暴風雨で南大門、鐘楼が倒壊したりといった事件が起こるが、後に皇族・貴族の崇敬を受けて黒田庄に代表される多数の荘園を寄進されたり、開発した。