Muryojufuku-ji Temple is said to have been founded by bodhisattva Gyoki in 749-757 at the order of Emperor Koken. It was further developed around 1264 by Ojun Gyonen, a monk from Iga Province. During the Kamakura era, it flourished as one of the major temples in the area and once was a training center for religious Shugendo practitioners and ascetic monks. These practitioners and monks in training are believed to be one of the origins of ninja.
According to the ""Iranki"" that summarizes the Tensho Iga War, in order to oppose the construction of Maruyama-jo Castle in 1578 by Takigawa Saburohyoe, Oda Nobuo’s vassal, the Iga clan gathered at Mt. Tendo-zan (located across Kizugawa River on the opposite side of Maruyama-jo Castle) to discuss how to immediately attack and take over the castle. When Nobuo Oda invaded Iga Province in 1579, the Iga clan gathered at Heiraku-ji Temple, Terada Daiko-ji Temple, and Mt.Tendo-zan to hold discussions and defeated Oda's army twice.
In September 1581, Oda Nobunaga invaded Iga Province from Shigaraki, Koka, Kabuto, and Yamato. Mt. Tendo-zan, one of the military bases belonging to the Iga clan, was attacked by the armies of Oda’s three generals. The main hall, Goma-do Hall, and guest halls were all destroyed by fire during this attack and not rebuilt until the Edo era.