Ernest Baker obtained the degree Bachelor of Science (BSc) and entered the public service of the Union of South Africa in December 1912, when he was appointed on probation as an assistant district forest officer. In April the next year he became a lecturer in botany at the Cedara School of Agriculture in Natal, where he remained to 1917. In that year he was appointed as agricultural botanist at the Agricultural School, Elsenburg (near Stellenbosch), a post he held until 1926 when the school was amalgamated with the Faculty of Agriculture at the University of Stellenbosch to become the Stellenbosch-Elsenburg College of Agriculture. During his years at Elsenburg he participated in crop and pasture research.
Baker became a foundation member of the South African Biological Society in 1917.