In 1211, Hojo Masako founded "Zenjo-in" on Mount Koya to pray for the repose of her late husband Minamoto no Yoritomo (who died in 1199). At the time, Masako was the de facto leader of the Kamakura shogunate as the "nun shogun," and she had a portion of Yoritomo's remains divided and enshrined on Mount Koya, establishing this temple as his memorial. In 1223, the temple was renamed Kongo-sanmai-in to also commemorate Minamoto no Yoriie and Sanetomo, and the Tahoto pagoda (National Treasure) was built that same year. The temple stands as an important Kamakura-period heritage that conveys to the present day Masako's deep love for Yoritomo and her prayers for the repose of three generations of the Minamoto.

Minamoto no Yoritomo (1147-1199) — founder of the Kamakura shogunate. After his death in 1199, his principal wife Hojo Masako continued to govern as the de facto leader of the shogunate. In 1211, she founded this temple (originally Zenjo-in) on Mount Koya to pray for Yoritomo's repose, and tradition relates that she divided and enshrined a portion of his remains here. A memorial pagoda for Yoritomo also stands in the precincts, making this temple one of the few Mount Koya subtemples enshrining the spirit of the founder of the Kamakura shogunate, and a center of Minamoto veneration.

Minamoto no Sanetomo (1192-1219), the third shogun of the Kamakura shogunate, was assassinated by Kugyo at Tsurugaoka Hachimangu in 1219, becoming the last of the Minamoto shogunal line. In 1223, on the occasion of Yoritomo's 24th memorial, his mother Hojo Masako renamed this temple Kongo-sanmai-in to also commemorate Sanetomo and Yoriie. A memorial pagoda for Sanetomo stands in the precincts, making this a place of repose conveying the tragedy of three generations of the Minamoto.