In 1905 he was appointed full professor at the University of Nebraska, but left in 1907 to head the botany department at the University of Minnesota in Minneapolis. From 1917 to 1941 he was employed as an ecologist at the Carnegie Institution of Washington in Washington, D.C., where he was able to carry out dedicated ecological research. While employed at Carnegie Institution of Washington, Clements faced criticism for his experiments conducted with the purpose of creating new plant species. Due to these criticisms and as well as personal conflicts with his co workers, in 1920's the title of director of research in experimental taxonomy was given to Harvey Monroe Hall.