In 1898 he bought a copy of the Codex Troano. This triggered his interest in Maya culture. In 1900 he retired from his work in printing. He relocated to San Diego, California. He became involved in theosophy. He moved to a theosophy colony called the Aryan Theosophical Colony. It was located in Point Loma, a neighborhood of San Diego. He started teaching antiquities at the colony college. While teaching, he researched and published about Mayan culture and language. He started building his own collection of Mayan documentation, including manuscripts and photographs of manuscripts. By 1910 he had published the Paris Codex. Two years later, he started exploring how comparing different Mayan languages could help make further discoveries about Mayan hieroglyphs. He departed from New Orleans in June 1917 to visit Guatemala for archaeological research. He started, and served as president of, the Maya Society at Philadelphia in 1920. He started working for the Archaeology Commission of the Maryland Academy of Science as a consultant. The following year he became a researcher at the Carnegie Institution for Science. He discovered a monument dating from 120 BC in on while on a trip in Guatemala. This is credited with solidifying that the Mayan culture was older than originally thought. In 1922, he started working for the Republic of Guatemala as director-general of their archaeology department. He was also the director of the archaeology museum there. Gates was living in Charlottesville, Virginia and traveled to Guatemala, too. After one visit in 1922 he returned to Charlottesville with a K'iche' man he had met. In Charlottesville, Gates studied the K'iche' language using a wave writer. In 1924, Gates became director of the American Indian Defense Association. That year, Tulane University bought half of his Mayan archives. He also started working for Tulane in their Middle American Research department. Gates would, by 1930, sell his farm in Charlottesville, allowing him to sustain his research. He published the first and only issue of the Mayan Society in 1930 through Tulane. It was received poorly by faculty at Tulane and never published again. Gates also published various codices, including the Dresden Codex and Madrid Codex. He was also highly active in developing education and land policies while working for the United States Bureau of Indian Affairs in 1934.
Later life and legacy
acquired the other half of Gates Mayan archives in 1936. The following year, Gates relocated to Washington, D.C. He worked at the Library of Congress and published three editions of A Grammar of Maya in 1938. Gates died in Baltimore, Maryland in 1940. Works by and collections once owned by Gates are held in the collections of Brigham Young University.