Chamberlain organized and directed the botanical laboratories at the University of Chicago (1897–1931), where he became professor of plant morphology and cytology (1915). With plants collected in Mexico, Australia, New Zealand, South Africa, and Cuba, he created in the university greenhouses the world's foremost collection of living cycads, which remained unsurpassed until a decade after his death. With the U.S. botanist John Coulter he prepared textbooks on the morphology of spermatophytes (1901), angiosperms (1903), and gymnosperms (1910). He also wrote The Living Cycads (1919) and Gymnosperms, Structure and Evolution (1935).