In 1591, Toyotomi Hideyoshi granted the 11th Honganji head Kennyo the current Horikawa-Rokujo site, enabling his final relocation from Tenma. After the Ishiyama War defeat, Kennyo had wandered from Saginomori in Kii to Kaizuka in Izumi to Tenma — and establishing a new head temple in Kyoto had been his long-cherished wish. Kennyo passed away the following year in 1592 at age 50. This grant of land became the foundation of Nishi Honganji that continues today. It was the final great project of Kennyo"s life, and 11 years after the withdrawal from Ishiyama, the Honganji institution at last secured its permanent headquarters.

In 1207, Shinran was exiled to Echigo along with his master Honen in the Jogen Persecution. After pardon, he spent over 20 years propagating in the Kanto region. He died in Kyoto in 1262 at age 90. His great-granddaughter Kakushinni built a mausoleum at Otani, the origin of Honganji. Shinran's teachings center on 'akunin shoki' (the wicked are the true object of Amida's salvation) and 'tariki hongan' (salvation through Other Power). Today, Jodo Shinshu is Japan's largest Buddhist denomination, with Honganji-ha (Nishi Honganji) alone having approximately 10,500 branch temples.

In 1586, Hideyoshi donated the current site to Honganji, initiating the construction of the grand temple complex. The Karamon gate and Hiunkaku pavilion are masterpieces of Momoyama culture relocated or built under his orders. Hideyoshi's protection of Jodo Shinshu made Nishi Honganji a base for nationwide expansion of the sect.