At this point, he made a definitive transition to civilian life by taking up the chair of "transcendental mathematics" at the new École centrale.

Over a period of 22 years, the Annales de Gergonne published about 200 articles by Gergonne himself, and other articles by many distinguished mathematicians, including Poncelet, Servois, Bobillier, Steiner, Plücker, Chasles, Brianchon, Dupin, Lamé, even Galois.

In 1813, Gergonne wrote the prize-winning essay for the Bordeaux Academy, Methods of synthesis and analysis in mathematics, unpublished to this day and known only via a summary.

He called for the abandonment of the words analysis and synthesis, claiming they lacked clear meanings.

He published his "Essai sur la théorie des définitions" (An essay on the theory of definition) in his Annales in 1818.