Each student in grades six through eight will successfully navigate coursework in English, History, Mathematics, Science, Spanish, Art, Music, and Physical Education. In addition to student-centered classroom activities, Middle School students have a number of extra-curricular activities available to them. Additionally, students participate in an athletics program that emphasizes the philosophy of inclusion and teamwork.

The Middle School years are ones of great transition, challenge, and maturation. They are also a time of intense curiosity which Allen Academy encourages. The school emphasizes a gradual and constructive release of responsibility to students while maintaining a balance of academic and social autonomy in all programs.