After leaving the Navy, Beale returned to California as a manager for W. H. Aspinwall and Commodore Stockton, who had acquired large properties there. In 1853, President Fillmore appointed Beale Superintendent of Indian Affairs for California and Nevada. Congress appropriated $250,000 to improve native conditions in Beale's district. On his way to California, Beale left Washington on May 6 with a party of 13 and surveyed a route across Colorado and Utah to Los Angeles, California, for a transcontinental railroad. He reached Los Angeles on August 22. Beale served as Superintendent until 1856. California Governor John Bigler appointed Beale a brigadier general in the California state militia to give Beale additional authority to negotiate peace treaties between the Native Americans and the U.S. Army.