Haynes took a job teaching at the Jay County public school after returning home. Soon his income allowed him to buy a home near Portland High School where he worked and was promoted to principal in 1882. That summer he took a week-long trip to visit Bertha in Chattanooga, Tennessee, where he became sick with a cold and spent most of his time in bed nursed by Bertha, learning that her family would be returning to live in Portland in 1883. After returning from the trip, he continued saving money and in 1884 he decided to continue his education by enrolling at Johns Hopkins University in Baltimore, Maryland. He chose the school because, as it was only eight years old, it had one of the most modern laboratories available. He took courses in chemistry and biology and learned advanced metallurgic techniques. His mother died in May 1885 and he decided to leave the university without completing his second year, as he was not working to attain a degree but only taking courses of interest. After he had returned home again, he took a position at the newly established Eastern Indiana Normal School and Commercial College (now Ball State University) and served as the head of the chemistry department.