Upon his return from Paris, Mathews taught life classes at the San Francisco Art Students League and the CaliforniaSchool of Design. He became director of the latter in 1890, and in 1894, married Lucia Kleinhans, one of his art students. Although he was occasionally criticized for his autocratic approach to teaching, which was based on the French paradigm for the Barbizon school, he vigorously supported the presence of female students at the School of Design and published in 1891 a rebuttal to Emil Carlsen, a former Director of the school, who declared that women pupils were inferior and indifferent students. In 1904 the San Francisco District Attorney compelled Mathews, in his capacity as the school's Director, to investigate charges brought by Albert DeRome that he was seriously injured in a hazing ritual devised by fellow student Armin Hansen. He continued to teach there until shortly after the great 1906 San Francisco earthquake. Following the earthquake, he and his wife Lucia collaborated with the entrepreneur John Zeile to open the Furniture Shop in San Francisco. There he could unleash his combined skills as a craftsman, designer and painter. Mathews and Zeile also established Philopolis Press and published the monthly Philopolis magazine, which promoted Arts and Crafts aesthetics in the rebuilding of the city. Among his many mural commissions was a twelve-panel series in the State Capitol Building in Sacramento. Other major commissions included murals for the Oakland Public Library, the Mechanics' Institute Library, the Lane Medical Library at Stanford University's medical school campus in San Francisco, the Supreme Court Chambers of the California Supreme Court Building in San Francisco, and the Court of Palms at the Panama-Pacific International Exposition. The Mathews mural Vision of Saint Francis, originally created for the Savings Union Bank in San Francisco, is now in the collection of the Crocker Art Museum. In the late 19th and early 20th centuries Mathews and his wife frequently sketched on the Monterey Peninsula and in 1907 he helped organize the inaugural exhibition at the Hotel Del Monte Art Gallery. At this time Mathews joined William Keith in opposing the restoration of the Spanish missions in California, which Edwin Deakin vigorously campaigned to restore as functioning religious communities.
Death and legacy
He died at his home in San Francisco in 1945. Mathews was a master of many media: oil painting, watercolor, pastel, gouache and fresco. He and Lucia designed detailed interior decoration schemes in what became known as the California Decorative Style. They created a variety of furniture, boxes, carved and painted picture frames and many other decorative objects, and even large stained glass windows.