During his own post-graduate studies through Johns Hopkins in Baltimore, Maryland, Lewis taught Biology at Randolph–Macon College in Ashland, Virginia from 1905 to 1912. After he received his PhD, Lewis accepted a position as Assistant Professor of Botany at the University of Wisconsin. He then taught as Professor of Botany at the University of Missouri from 1914 to 1915. In 1915, University of Virginia president Edwin A. Alderman recruited Lewis, who became Professor of Biology and Agriculture, and began to modernize the institution and increase its research output. Lewis became popular at the University, as well as important in the state's scientific community—helping to found the Virginia Academy of Science and serving as its first president. Lewis was appointed Dean of the University in 1934 and, Dean of the College of Arts and Sciences in 1946, a position he held until his retirement in 1953. He is buried at the University of Virginia Cemetery. Lewis's signature course was Biology C1: Evolution and Heredity. He provided much of the scientific rationale for the eugenics movement now best known for the discredited legal decision in Buck v. Bell. In the 1920s, Lewis championed the state's Anglo-Saxon clubs as staving off apocalyptic "racial decay", including giving a lecture "What Biology Says to the Man of Today." Lewis thus worked with alumnus John Powell, Major Earnest S. Cox and Dr. Walter Plecker. Later, he consistently advised against hiring academicians who might question his group of eugenicists, or advocate environmental solutions to social problems, or even critically examine southern traditions, as well as criticized Jewish sociologists. Lewis had unsuccessfully opposed admission of Gregory Swanson, who matriculated at the University's Law School in the fall of 1950 pursuant to a federal court order after the NAACP victories in Sweatt v. Painter and McLaurin v. Oklahoma, but Swanson left about a year later after encountering the "overwhelming climate of racial hostility and harassment" he had experienced. Thus Walter N. Ridley, a professor at Virginia State College who arrived a semester after Swanson actually became the first recipient of a postgraduate degree at UVA. During Virginia's Massive Resistance crisis, mostly after his retirement, Lewis attempted to "hold the line" and limit desegregation to token individuals, taking an active part in the radical Defenders of State Sovereignty and Individual Liberties. Lewis was a fellow of the American Academy of Arts and Sciences, and served as president of the American Society of Naturalists, American Biological Society, and the Botanical Society of America.