Doneau accepted a call from the Reformed Elector Palatine Frederick III to a professorship at Heidelberg and assumed the post in early 1573.

Doneau returned to Germany and became professor of law at the Altdorf Academy (the university of the Free Imperial City of Nuremberg).

However, while many of the followers of this so-called mos Gallicus (French method) concentrated on a critical evaluation of the texts in the Corpus Iuris Civilis, Doneau was more interested in the construction of a coherent system of law.

His best known work Commentarii de iure civili (commentaries on the civil law) (in part edited posthumously by Scipione Gentili) is one of the first attempts to organise the subject matter of Roman law in a logical order rather than according to the sequence of the books and titles of the Digest.

Doneau also made major contributions to various specialised areas of law such as the doctrine of possession and acquisition of ownership.