In around 1495, after Cloistered Imperial Prince Jiun of Daisojo (high priest), who was the son of Imperial Prince Fushiminomiya Sadatsune and an adopted child of Emperor Gotsuchimikado, became the twenty-sixth monshu and entered the temple, it became a custom for a member of the Imperial family to serve as a monshu in Manshuin Temple, and the position as miya-monzeki (temples headed by imperial princes) was established.
明応4年（1495年）頃、伏見宮貞常親王の息で後土御門天皇の猶子である大僧正慈運法親王が26世門主として入寺して以降、曼殊院は代々皇族が門主を務めることが慣例となり、宮門跡としての地位が確立した。