The AJHS has utilized a house system since 2016, labeled as "support systems for formation" aimed at "intensifying the care and formation the school bestows upon its students." The AJHS is divided according to the following four clusters, named after pivotal places in the life of Saint Ignatius of Loyola: Cardoner, La Storta, Montserrat, and Pamplona. Sections from Grade levels 7-10 are divided equally and placed in their respective clusters. Each cluster has dedicated class moderators, subject teachers, guidance counselors, immersion coordinators, and staff to cater to the specific needs of the students. The cluster is led by a "cluster coordinator" (teacher) and cluster head(student), who organize a variety of activities, such as mentorships and team building. The cluster system idea came from a study of Dra. Carmela Oracion done with regards to school systems in Singapore, where results showed cluster systems benefited students more than the traditional batch systems.