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.

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.

Stoll also collected modern art, including paintings by Ferdinand Hodler.