After completing his degree, Chandler returned to the United States to pursue his own scientific career. Upon his return, in 1857, Chandler became the chemical assistant at Professor Charles Joy's laboratory at Union College in Schenectady, New York, and shortly thereafter began to lecture on Mineralogy and Geology at the college as well as manage the laboratory. He became an associate professor at the College in 1857 at the age of 21. Shortly after, he and his younger brother William became members of The Kappa Alpha Society, of which Joy was also a member. He remained at Union College for the next 7 years during which time he ran the chemistry lab and married his first wife, Anna Craig Chandler.