In 1531, a conflict within the Hongan-ji religious group occurred (it is called the Kyoroku-Tenbun War (Kyoroku-Tenbun Rebellion) including the later incidents until when Yamashina Hongan-ji Temple was burned down), but Syonyo resolved this conflict and made efforts to strengthen the leadership of Hoshu (high priest).
1531年には本願寺教団内部で対立（後の山科本願寺焼討事件まで含めて享禄・天文の乱と呼ぶ）が起こるが、証如はこれを抑えて法主の指導力強化に努めた。