He returned to the United States near Boulder, Colorado in 1935, and then in late 1946 settled in Los Angeles, California with his wife Alice and their three sons, Eugene, Robert, and Richard. In Orange County, Naka and four friends founded a bonsai club in November, 1950, which is known today as the California Bonsai Society. He became a very important force in American bonsai art in the 1950s-60s. He was a driving force in the spread of bonsai appreciation and the practice of bonsai art in the West and elsewhere. Naka traveled and taught extensively around the world, at conventions and clubs, but refused to hold classes in Japan (where bonsai had been highly developed along certain lines over the centuries), saying "They want me to teach, and I tell them it's like trying to preach to Buddha."
A very few of his many accomplishments are the following: He published two books, entitled Bonsai Techniques I and Bonsai Techniques II, texts that are revered as being the bibles of western bonsai to many artists. These books would be translated into French, German, Italian, and Spanish by 1990. He contributed articles, forewords, and photographs to a number of specialty magazines and books. Nina S. Ragle's compilation of 287 proverbs presented in both Japanese and English from Naka, Even Monkeys Fall Out of Trees, was published in 1987. (The title refers to the little recognized fact that, yes, even bonsai masters can make a mistake.) He was a founding director of the World Bonsai Friendship Federation (WBFF) and a co-signer of the Constitution of the Latin-American Bonsai Federation (LABF). He was an honorary advisor to the National Bonsai Foundation. Naka was chosen in 1992 as one of thirteen honorees to receive a National Heritage Fellowship, the first bonsai artist to receive this prestigious award. At the time he received his Fellowship, he said, "It has a beginning but no end. A bud today becomes a branch tomorrow." He was awarded a 1992 National Endowment for the Arts fellowship.
Other quotes of his included "Bonsai is not the result: that comes after. Your enjoyment is what is important"; "It must have philosophy, botany, artistry, human quality behind it to be a bonsai"; "The bonsai is not you working on the tree; you have to have the tree work on you"; and "Leave room for the birds to fly through" the branches of your bonsai. Of Naka's many works, the most recognizable composition is Goshin, which means "protector of the spirit." It is a group planting of eleven foemina junipers, each tree placed to represent one of Naka's grandchildren. The planting can be seen on display at the National Arboretum. About a month before he died, Naka donated his very first bonsai, a Montezuma Cypress, to the National Bonsai and Penjing Museum. In May 2005, a collection of over 80 of his drawings of how he envisioned the future development of various workshop participants' trees was published as John Naka's Sketchbook, edited by Jack Billet and Cheryl Manning.
On May 23, 1960 Japan's Minister of Foreign Affairs, Shunichiro Fujiyama presented Mr. Naka with an honorary citation from the Japanese government for his effort in promotion of goodwill and friendship between Japan and the United States.
On November 24, 1967 Mr. Naka received an honorary medal and citation from the President of Japanese Agricultural Affairs Department, Prince Norihito Takamatsu and Eikichi Hiratsuka.
On May 20, 1972 the County of Los Angeles' Supervisor Mr. Ernest E. Debs presented Mr. Naka an honorary citation on behalf of the County for "his outstanding contributions to the Japanese-American friendship by providing the people of Los Angeles and the nation with ability to understand and appreciate the beauty and significance of bonsai culture."
- Joy Buchanan (May 24, 2004). "John Y. Naka, 89; Brought Art of Asian Bonsai to the West". The Los Angeles Times.
- Bonsai Techniques I, ISBN 0-930-422-31-7
- John Yoshio Naka, In Celebration of a Grand Master's Life
- NABF Newsletter #1, A Tribute to John Naka
- The Art of Bonsai Project, A Tribute to John Yoshio Naka
- "John Y. Naka", Bonsaitalk