The JAE carried out its activities in many centers that put into practice the interdisciplinary approach of its reform plan. The lab was its main venue. Its two flagship centers were the National Institute of Sciences and the Center for Historical Studies. The first conducted high research into the natural sciences, incorporating existing facilities like the National Science Museum, the Botanical Garden, the Marine Biology Center, in Santander, and creating new ones like the Physics Research Laboratory.  The Center for Historical Studies focused on the humanities.

The Residencia de Estudiantes was a singular institution of the JAE. It was a research center and became a cultural reference in its time. Prominent figures from the arts and sciences helped to transform the Residencia into a European avant-garde hub. The Residencia de Señoritas followed a similar pattern, with its cutting-edge Foster laboratory and its commitment to women’s education through cultural activities and initiatives such as courses in librarianship.

Last but not least, the school was a key element in the educational mission of the JAE.
It established pilot schools such as the Instituto-Escuela in Madrid, Barcelona, Valencia, Sevilla and Málaga, and the Grupo Escolar Cervantes.