After his arrival at Oxford and during World War II, Cornforth significantly influenced the work on penicillin, particularly in purifying and concentrating it. Penicillin is usually very unstable in its crude form; as a consequence of this, researchers at the time were building upon Howard Floreys work on the drug. In 1940, Cornforth and other chemists measured the yield of penicillin in arbitrary units to understand the conditions that favoured penicillin production and activity, and he contributed to the writing of The Chemistry of Penicillin'.
In 1946, the Cornforths, who had by now married, left Oxford and joined the Medical Research Council (MRC), working at the National Institute for Medical Research (NIMR), where they continued on earlier work in synthesising sterols, including cholesterol. The Cornforths' collaboration with Robinson continued and flourished. In 1951, they completed, simultaneously with Robert Burns Woodward, the first total synthesis of the non-aromatic steroids. At the NIMR, Cornforth collaborated with numerous biological scientists, including George Popják, with whom he shared an interest in cholesterol. Together, they received the Davy Medal in 1968 in recognition of their distinguished joint work on the elucidation of the biosynthetic pathway to polyisoprenoids and steroids.
While working at the MRC, Cornforth was appointed a professor at the University of Warwick and was employed there from 1965 to 1971.
In 1975, Cornforth was awarded a share of the Nobel Prize in Chemistry, alongside Vladimir Prelog. In his acceptance speech, Cornforth said:
Also in 1975, he moved to the University of Sussex in Brighton as a Royal Society Research Professor. Cornforth remained there as a professor and was active in research until his death.