Bowen married three times: first to Actress Sonia Sorel (1921–2004). The marriage ended in divorce. His second wife was Martine. His third marriage, to Isabella Bowen, lasted until his death. He is survived by his sons Michael, Ramakrishna and Indra, and daughters Maitreya and Kaela.

Michael Bowen was born December 8, 1937 in Beverly Hills to Grace and Sterling Bowen. His father was a dentist. His mother's lover was Benjamin (Bugsy) Siegel, affectionately known as "Uncle Benjie", who would often take the youthful Bowen to not only the Flamingo Hotel on the Las Vegas Strip in Paradise, Nevada that he created, but also to the Sir Francis Drake Hotel near Union Square in downtown San Francisco. Bowen's early romance with San Francisco established this city as his home base from which he would frequently travel to other places in the world.

Michael Bowen moved to San Francisco in the late 1950s, and along with fellow Artist comrades Arthur Monroe and Michael McCracken, lived and worked out of 72 Commercial Street. Painting spontaneous, impromptu, hectic canvases, along with assemblage and collage, Bowen became an integral part of the San Francisco Renaissance.

An icon of the American Beat Generation and the 1960s counterculture, Bowen is also known for his role in inspiring and organizing the first Human Be-In in San Francisco. Chronicled in books and periodicals reflecting on the turbulent 1960s, Bowen's historical impact on both the literary and visual art worlds is well documented. He remains influential among avant-garde art circles around the world.

In 1963, on one of Bowen's visits to be with his mentor in Tepoztlan, he was initiated into an ancient Aztec shamanic ceremony that inspired his Future work with world consciousness transformation. After his initiation, Bowen traveled to New York City, where he established a studio in the Lower East Side and met with many of the Beat Generation artists, Writers, and Musicians living on America's East Coast. He often visited the two former Harvard professors Timothy Leary and Ram Dass, then Richard Alpert, in their mansion at Millbrook, New York, where a new variety of consciousness experimentations were being conducted.

On October 6, 1966, Bowen and Cohen organized the Love Pageant Rally, a celebration against the new law criminalizing LSD in California. Because of Bowen's friendship and invitation, Janis Joplin came to the event along with her band, Big Brother and the Holding Company, and played for free. About 3,000 people attended the Love Pageant Rally, and towards the end, Ram Dass, Cohen, and Bowen discussed having another event, this time much bigger, to celebrate the newly developing hippie counterculture and consciousness expansion in San Francisco.

On October 21, 1967, 75,000 anti-war protesters surrounded the Pentagon in Washington D.C.. On that day, Bowen organized 200 lbs. of daisies, purchased by his New York friend Peggy Hitchcock (wife of Walter Bowart) to be dropped from a light aircraft onto the Pentagon, but the FBI heard of the plan and seized the aircraft, so the flowers were distributed to the protesters as the Military Police protected the Pentagon from the massive anti Vietnam War demonstration. The daisies, brought to the front lines of the tense confrontation by Bowen and others, were taken by the demonstrators and put into the nearest holder that symbolically communicated their anti-war sentiment.

The iconic photograph "Flower Power", taken by photojournalist Bernie Boston, of the daisies being put into the bayoneted gun barrels of the Soldiers by the unarmed anti-war demonstrators, was nominated for a Pulitzer Prize in 1968. The photograph "flower power" is listed as #30 among the top 100 wartime photographs and the idealism of flower power remains as an anti-war symbol.

In 1969, Bowen made his first pilgrimage to India and Nepal where he completed a series of drawings and sketches. These drawings were made into a book, Journey to Nepal, published by City Lights Books in 1970.

In the early 1990s, Bowen found an abandoned cement traffic barrier in Golden Gate Park and claimed to have transformed it into a Shiva lingam. It then became a site of worship and veneration until the authorities had him remove it. At that time, he was known as Baba Kali Das.

His style progressed from large abstract expressionist canvases to figuratives and large faces, to assemblage. Bowen's painting about McCarthyism, Red Future? from the Wennesland Collection, was featured in the 1995 Whitney Museum exhibition Beat Culture and the New America, 1950-1965, which opened in New York City, and then traveled to the Walker Art Center in Minneapolis and the De Young Museum in San Francisco, California.