By 1912 he took a job with the United States Department of Agriculture, where he would stay for the next thirty years. Baker's work was noticed rather quickly, in part because of his contributions to the Yearbooks from 1915 to 1938, several of which he edited. For the first eighteen years at the USDA he was devoted to studying the geographical aspects of land use. One of his first works, co-authoring Geography of the World's Agriculture (1917) with Vernor Clifford Finch, led him to even wider recognition. Shortly after its publication, Baker returned to the University of Wisconsin-Madison for further graduate study, in economics, and earned his Ph.D. in 1921 with a dissertation on land utilization. While there, Baker had been influenced by Henry Charles Taylor and Richard T. Ely, two notable economists, to shift his work more toward the economic aspect of geography and agriculture. In 1922 he joined the USDA's new Bureau of Agricultural Economics, headed by Henry C. Taylor. With the success of the Geography of the World's Agriculture, he instigated work on the Atlas of American Agriculture, on which he himself was planner and editor. The massive work was released in six parts between 1918 and 1936.
Baker acted as a part-time professor at Clark University from 1923 to 1927, and later gave several series of lectures at other universities. With the appearance of the journal Economic Geography, Baker became associate editor, and later a contributor of a notable series of articles on regional agricultural geography of North America. His interest in farm populations started around 1920, however it was during the 1930s that this field became a major focus of the USDA. Baker was particularly interested in the migration of rural youths into urban areas. Even into his later years, populations problems occupied much of his research and energies. Baker recognized that only a minority of the world's population lived under decent living conditions. He turned his attention to improving standards for American farmers. He hoped to achieve this by raising the level of appreciation for farmers and their contributions within the United States, and studying recent trends to aid in planning and forecasting potential problems. He also tried to encourage Americans to have larger families in order to ensure successful future generations in the country.
Baker had been critical of many aspects of urban life, and collaborated with Ralph Borsodi on Agriculture in Modern Life (1939), advocating a return to rural living. He himself however suggested more of a "rurban" lifestyle, which combined aspects of both urban and rural life. He married in 1925 to Alice Hargrave Crew. They had four children together and raised them in a suburban area with much land where they were able to raise chicken and cows and have a garden. He later bought a large farm where he could take up his interest in soil conservation.
Having suffered from health problems his entire life, he died in his home in College Park, Maryland.