In 2017, he returned to India, assuming the role of a full professor in the Department of Zoology at Banaras Hindu University, Varanasi. Chaubey's research primarily focuses on understanding the peopling of South and Southeast Asia, with a keen interest in various ethnic groups such as the Andaman, Austroasiatic, Indian Jews, Siddi, Roma, and Parsis. Employing a combination of genetic markers and computational tools, he investigates the impacts of migration, genetic drift, and selection on the demographic history of South Asia while also contributing to the development of new analytical methodologies.