In 1866, Abbott resigned from service to the Union Army and returned to Canada. He attended primary medical classes at the University of Toronto the following year. While he did not graduate, he established a medical practice and was admitted to the College of Physicians and Surgeons of Ontario in 1871. In an Anglican wedding ceremony in Toronto on 9 August 1871, he married Mary Ann Casey, the 18-year-old daughter of a successful Black barber. Abbott and his wife moved to Chatham where he resumed his medical practice. They eventually had three daughters and two sons.