In 1478, the 8th Honganji head Rennyo — returning to Kyoto from Yoshizaki — resolved to rebuild Honganji at Yamashina, spending over a decade constructing a magnificent temple complex. Since the destruction of the Otani Honganji by Enryakuji monks in 1465, the Honganji had wandered without a permanent home; here at last it obtained its enduring headquarters. Yamashina Honganji formed a massive moated, earthwork-walled temple town that functioned as the institutional headquarters directing Ikko-shu followers nationwide. Rennyo devoted himself here to composing his "Ofumi" pastoral letters and organizing the network of followers, completing the work that made Jodo Shinshu the largest Buddhist denomination in Japan. Rennyo died here at age 85 in 1499. His mausoleum still stands adjacent to the Yamashina Honganji ruins. The life of Rennyo, the great restorer of Honganji, was consummated in the completion of Yamashina Honganji.

A Honganji stronghold built by Rennyo in 1478, where the image of Shinran transferred from the Otani Mausoleum was enshrined as the principal object of worship and center of Ikko-shu proselytizing.