In 1920 he was appointed Dean of Faculty at the University of California, Berkeley, but he left that same year to become president of the Carnegie Institution in Washington, D.C.. His departure caused the university to combine the Paleontology Department with the Geology Department, angering Merriam's benefactress, Annie Alexander, who subsequently founded and endowed the university's Museum of Paleontology. As the head of Carnegie Institution, Merriam's administrative duties led to a reduction in his research for the rest of his career. He accomplishments as president included helping to advance the educational programs of the National Park Service, as well as helping to preserve the California redwoods. His published papers are collected in a four-volume set published in 1938 by the Carnegie Institution.