Antai-ji was founded in 1923 by Oka Sotan as a monastery for scholars to study the Shōbōgenzō. At that time, it was located in northern Kyoto and many leading scholars studied there. Vacated during World War II, Sawaki Kodo (1880-1965) and Kosho Uchiyama (1912-1998) moved into Antai-ji in 1949, and made it a place for Zazen. During the late sixties, the name of this small temple became known both in Japan and abroad for its practice of Zazen and formal begging.
The increase of visitors and the many new houses being built around the temple created much noise, which made it difficult for the practice of Zazen to continue at the Kyoto location. Therefore the following abbot, Watanabe Koho (b. 1942), decided to move Antai-ji to its present location in northern Hyōgo. Together with the quietude of the mountains, he was looking for a new life style that would bring Zen back to self-sufficiency. The former abbot Miyaura Shinyu (1948–2002) protected this quiet life of Zazen while putting the ideal of a self-sufficient monastery into practice, until his sudden death in the snow in February 2002. His disciple, the German monk Muho Noelke (b. 1968), continues as the present abbot.