After completing his PhD, Bays took up a post teaching history at the University of Kansas, directing the Center for East Asian Studies and becoming a full professor in 1985.[3] After working there for thirty years, in 2000, Bays moved to the History Department of Calvin College, where he held the Spoelhof chair from 2000–2002.[4][5] He retired from Calvin College in 2012 and was appointed as professor emeritus, though he relocated with his wife Janice to Kansas City, Missouri.[1]
In 1984, when Bays was a Fulbright scholar in Taiwan, he received a letter from the historian of China, John K. Fairbank, who encouraged him to conduct a more systematic study of Christianity in China, a topic Bays had recently begun work on. This would lead to his launch of the History of Christianity in China Project, which resulted in the edited volume Christianity in China: From the Eighteenth Century to the Present, published in 1996.[6]