ENISE, via its association with ECL, is one of the coaccredited institutions within the site doctoral school ""Sciences Ingénierie Santé"" (ED SIS 488), which is a multidisciplinary school covering the following fields: Sciences Pour l’Ingénieur (engineering), Sciences et Technologies de l’Information et de la Communication (ICT) and Sciences de la Santé (health).
Within this doctoral school, ENISE delivers a PhD of Université de Lyon together with École Centrale de Lyon. ÉNISE participates in its gouvernance and organisation along with Université Jean Monnet and École des Mines de Saint-Étienne. ENISE's lecturers and researchers supervised approximately 50 theses in 2019 (including those of about 30 students of EDSIS).