In 1921 Gilbert-Carter returned to Cambridge to take up his position as Director of the University Botanic Garden and Curator of the Herbarium at the Botany School where he taught at the age of 37. Within a year he had published his first book, Guide To The Botanic Garden Cambridge (1922), followed by his Descriptive Labels for Botanic Gardens (1924). The gardens were much depleted, because of the war but his friendship with Reginald Cory, a fellow alumnus, resulted in considerable funding including the building of Cory Lodge as a residence for the Director.
Amongst his students, Donald Piggott, would later become a professor in the Botany School, and director of the garden (1984–1995). Gilbert-Carter is remembered by the Gilbert Carter Woodland in the Garden.