The museum was the dream of Mihoko Koyama (after whom it is named), founder of the religious organization Shinji Shumeikai[1] which is now said to have some 300,000 members worldwide.

Meanwhile, the Church of World Messianity (世界救世教, Sekai Kyūseikyō), the parent organization from which this Shumeikai came, had opened the "stunning" MOA Museum of Art in the mountains behind Atami in 1982.

[16] The museum's collection also includes Zo to kujira-zu byōbu (Elephant and Whale), a late masterpiece by Itō Jakuchū, one of Japan's most popular painters.

[22][23] In 2001 the museum acknowledged that a sixth-century statue of a Bodhisattva in its collection was the same sculpture which had been stolen from a public garden in Shandong province, China, in 1994, agreeing with the Chinese government to return it in 2007.

At the time of the agreement, the Chinese government publicly stated that the museum had purchased the Buddha statue in good faith on the open market and had not committed any fraud.

[29] The roof is a large glass and steel construction, while the exterior and interior walls and floor are made of a warm beige-colored limestone from France – the same material used by Pei in the reception hall of the Louvre.