Eschenmoser began his scientific career as a graduate student in the laboratory of Leopold Ružička, at the Eidgenossische Technische Hochschule (ETH) in Zurich. Ruzicka was a notable organic chemist himself having been awarded the Nobel Prize in Chemistry in 1939 for his work on the synthesis of androsterone and testosterone. Eschenmoser's early work on the cyclization of unsaturated, conjugated hydrocarbons directly contributed to advances in the field of terpene chemistry and provided insight into steroid biosynthesis.
 In the early 1960s, having become Professor of General Organic Chemistry at ETH, Eschenmoser began work on what was the most complex natural product synthesized at the time—vitamin B. In a remarkable collaboration with his colleague Robert Burns Woodward at Harvard University, a team of almost one hundred students and postdoctoral workers worked for many years on the total synthesis of this molecule. At the time, a significant obstacle to the synthesis of vitamin B had been the difficulty in the final macrocyclic ring closure necessary to complete the corrin ring structure at the center of the molecule. Eschenmoser and his collaborators discovered methods under which such  bonds between corrin ring building blocks could be formed, including a novel photochemical process which established the final junction of rings A and D with a high degree of stereospecificity, the key step in what was dubbed the "A/D variant" of the syntheses. Both the Harvard/ETH "A/B variant" and the ETH "A/D variant" of the syntheses were jointly and concomitantly completed in 1972, and they marked a landmark in the history of organic chemistry.
The Eschenmoser fragmentation, the Eschenmoser sulfide contraction and Eschenmoser's salt are named after him.