It was, however, after his return to Edinburgh to take up his father's old chair as Professor of Botany from 1888 to 1922 that Balfour left his mark, as he was also appointed 9th Regius Keeper of the Royal Botanic Garden Edinburgh. His father had greatly enlarged the botanical gardens during his tenure, but Balfour completely transformed them. Having put their finances on a safer footing by transferring them to the crown, Balfour engaged himself in a major reform of the gardens, establishing a proper botanical institute, and largely redeveloping the layout of the gardens to have a proper arboretum, building new laboratories and improving scientific facilities. He was awarded KBE in the 1920 civilian war honours list.