The University of Alcalá is organized around three main campuses that reflect its growth and academic diversification. Two of them are located in the city of Alcalá de Henares itself: one located in the historic center, which occupies emblematic buildings of the old Renaissance university complex, and another more modern one in the outskirts, known as the Scientific-Technological Campus, specialized in areas such as engineering, biomedicine and experimental sciences. The third campus is located in the city of Guadalajara, thus expanding the university's regional projection.

This multi-campus structure responds to an institutional reorganization approved by the university's Governing Council on October 2, 2012 and officially authorized by the Community of Madrid on October 29 of the same year. With this new organizational model, the University of Alcalá is articulated in 9 faculties and schools, 2 attached centers, 23 academic departments and 10 research institutes. This configuration allows for a broad educational offer, ranging from humanities and social sciences to technology, health and applied research, consolidating the university as an academic reference both nationally and internationally.