Born at Erstfeld in Switzerland, Eschenmoser was educated at the Federal Institute of Technology, Zurich, where he has taught since 1956 and where, in 1960, he was appointed professor of organic chemistry.

He is best known for his work in synthesizing a number of complex organic compounds. His first success came with colchicine – an alkaloid found in the autumn crocus – which has important applications in genetical research. He also collaborated with Robert Woodward on the synthesis of vitamin B_{1 2} (cyanocobalamin), which had first been isolated and crystallized in 1948 by the American organic chemist Karl Folkers (1906– ). Its empirical formula was soon established and in 1956 Dorothy Hodgkin established its structure. It took many years with samples passing between Zurich and Harvard before Eschenmoser and Woodward were finally able to announce its synthesis in 1965.