In 1912, he became a research assistant at the Kaiser Wilhelm Institute for Chemistry in Berlin, with Richard Willstätter, with whom he explored important insights on the importance of chlorophyll in carbon assimilation. In 1917, he was appointed professor of chemistry at the Ludwig Maximilian University of Munich. In the same year, he was hired as head of the pharmaceutical department of the Sandoz chemical factory in Basel (now Novartis).
In this company, he was president from 1949 to 1956, Director from 1964 he held the office of President of the Board.
Together with Sandoz employees, he developed a range of methods for producing drugs. Thus, he developed the first isolation of ergot alkaloids (as ergotamine and ergobasine) and cardiac glycosides, which are used as a medicine for heart diseases and migraines.
A continuous process for the production of soluble calcium salts was developed. He worked with Albert Hofmann.
Stoll also collected modern art, including paintings by Ferdinand Hodler.
Royal Society; German Academy of Sciences Leopoldina.