Born in the Saga Prefecture of Ky?sh?, Deshimaru was raised by his grandfather, a former Samurai before the Meiji Revolution, and by his mother, a devout follower of the J?do Shinsh? sect of Buddhism. Interested in the world, he abandoned his mother's practices and studied Christianity for a long while under a Protestant minister before ultimately deciding that it was not for him either. He returned to his own religion, Buddhism, and eventually came into contact with Rinzai teachings. Eventually, he also grew distant from Rinzai Buddhism and was unsatisfied by his life as a businessman. This led him to meet S?t? Zen Master Kodo Sawaki, whom he quickly became a disciple of. Deshimaru quickly followed in Master Sawaki's footsteps and devoted himself to the practice of Shikantaza.

Deshimaru was exempted from the army because of its short-sightness and went to Indonesia.

Deshimaru quickly rejoined his master and was by his side for fourteen years until Sawaki's death in 1965. Deshimaru received the monastic ordination shortly before Sawaki grew ill. Sawaki is said to have expressed his wish to spread Zen to other parts of the world on his death-bed, and asked Deshimaru to travel to Europe and spread the teaching.

In 1967, Deshimaru came to Europe and settled in Paris in order to fulfill his master's wish and spread the teachings of Zen. In the 1970s, his mission grew and he received dharma transmission from Master Yamada Reirin and became Kaikyosokan (head of Japanese Soto Zen for a particular country or continent) in Europe. He trained many disciples, and was the catalyst for the creation of a multitude of practice centers. His teachings and multitude of books helped spread the influence of Zen in Europe and America, particularly of the S?t? sect. He founded the AZI in 1970 and La Gendronnière in 1979. He died in 1982, after having solidly established Zen practice in the West.

After Master Deshimaru's death, three of his closest disciples, Etiene Zeisler, Roland Rech, and Kosen Thibaut, traveled to Japan to receive the shiho from highest Soto authority, Master Rempo Niwa.