At this timing, Shonyo began peace negotiations with Renjun who was called back from Nagashima in April, and Shonyo and Renjun were discharged by imputing the responsibility of having instigated this Ikki uprising to Shimotsuma brothers and, with the condition that they and all the followers in Kinai be excommunicated, the reconciliation between the bakufu, Hosokawa, and Rokkaku was achieved in November.
これを機に証如も4月に長島から呼び戻した蓮淳とともに和議を図り、下間兄弟を今回の一揆の扇動者としてその責任を転嫁することで証如・蓮淳の責任を不問とし、彼らや近江などの畿内門徒の総破門を行うことを条件にこの年の11月に幕府・細川・六角との和議が成立したのである。