Successive Minamoto clans had paid adoration to Mii-dera Temple from the fact MINAMONO no Yoriyoshi had been prayed for victory to the temple, and the temple cooperated when MINAMOTO no Yorimasa raised an army to defeat the Taira family and MINAMOTO no Yoritomo who defeated the Taira family protected the temple in return.
源氏は、源頼義が三井寺に戦勝祈願をしたことから歴代の尊崇が篤く、源頼政が平家打倒の兵を挙げた時にはこれに協力し、平家を滅ぼした源頼朝も当寺に保護を加えている。