While Amistad Academy's educational focus is on academic basics, its teachers also spend a significant amount of time teaching students organizational skills. The school's rigorous classroom atmosphere is an important part of this learning process, but these lessons extend to work done outside the classroom as well.

Every Amistad student must maintain a Homework Folder - a binder, structured like a personal organizer, with spaces provided to organize homework assignments for all of his or her courses by date. Students are responsible not only for doing their work, but for keeping a clear log of what they've accomplished, and for getting a parental signature on every evening's worksheet. The entire folder must be turned in each morning at 7:30, after which individual coursework is delivered to classrooms.