Shinzan Miyamae was born Nigata, Japan, in 1935. After graduation from Doshisha University with a degree in economics, he failed in three business ventures and experienced financial ruin. Contemplating suicide he was by chance transformed on reading a book on Zen. He was then 31. He was ordained a Zen monk by Mitsui Daishin Rōshi (1903–1992) who sent him to train at Shogenji monastery with his own master, the formidable Kajiura Itsugai Rōshi. Shogenji, known as the devil’s dojo, had the reputation of being the strictest training monastery in Japan. It was founded in the mountains of Gifu-ken on the spot where Zen ancestor Kanzan Egan (1277–1360) in his post-monastery training worked as a cow herder by day and sat zazen on a precipice by night. Recognizing his understanding, Itsugai Roshi wished Shinzan to succeed him at Shogenji. Shinzan Roshi instead went on to study the Tenryū-ji tradition of koan practice at Kokutai-ji (国泰寺) in Toyama in the north of Japan. The resident teacher, Inaba Shinden Roshi, requested Shinzan to become the next Zen Master of Kokutai-ji.
After completing his koan study, Shinzan Rōshi took the unusual step of visiting every Zen Master in Japan seeking to test and deepen his insight. He was unable to accept the monastery appointments indicated above due to resistance from other members of the Rinzai school who resented his vigorous stance against teachers without genuine insight.
Later he founded Zendo Kyodan (禅道教団 - Zenways Sangha), a primarily lay-based Rinzai organization  and restored Gyokuryuji, the hermitage of the great Zen master Bankei Zenji (1622–1693) with the intention of focusing on what he considered the true orientation of the Rinzai School, the development of spiritual insight.
He has become known for teaching outcasts and foreigners and protesting against institutional abuses. The Buddhist establishment in Japan considers him a maverick over his willingness to teach former members of the Doomsday Cult Aum Shinrikyo. Former senior member Kazuaki Okazaki converted to Zen Buddhism under Shinzan Rōshi’s guidance. Kazuki was found guilty of involvement in the murder of a lawyer and his family. Once his death sentence was confirmed, Japanese law only allows prison visits by family members. In order to continue teaching Kazuaki, Shinzan Rōshi adopted him as his son.
Long critical over the system of excessive charges for funerals (equivalent charges to $5–6000 US dollars are not unusual) Shinzan Rōshi withdrew from the Myoshinji branch of the Rinzai Zen School in 2005. In May 2007 he named Julian Daizan Skinner Rōshi as his successor, presenting him with inka. In November 2009 he also named Melody Cornell Eshin Rōshi as successor, presenting her with inka (transmission). 
In July 2015, the Zenways Sangha published the book "The Zen Character: Life, Art and Teachings of Zen Master Shinzan Miyamae" to coincide with Shinzan Rōshi's 80th birthday and an exhibition of his calligraphy in London. The book contains details of his artwork, together with a biography and excerpts from his teachings over the years.