Following this, Honno-ji Temple flourished as a sacred place from which Nichiren's 'Hommon-happon' Lotus Sutra doctrine was spread and, in the late medieval period, became one of the 21 head temples of the Kyoto Hokke Sect; gaining the protection of the Ashikaga clan.
その後、本能寺は日蓮の本義である「本門八品」の法華経弘通の霊場として栄え、中世後期には京都法華宗21ヶ本山の一つとなり、足利氏の保護を受けた。