Following the time of Kukai, his disciples Jichie and Shinzei served as head priests and guardians of the temple, but it eventually fell into decay during the late Heian period.
神護寺は、空海の後、弟子の実慧（じちえ）や真済が別当（住職）となって護持されたが、平安時代末期には衰退していた。