The academic philosophy of Bonita Springs Middle School ensures that each student has the opportunity to succeed. The school offers a multiple level approach to academics, serving students in tutorial and basic grade level classes, as well as, in advanced and "gifted" education classes. ESOL and ESE inclusion classes are also offered at each grade level.

Incorporating "hands-on" learning experiences inside and outside the classroom helps create an active learning environment. Environmental studies of Six Mile Cypress Preserve, Ding Darling Wildlife Refuge and the nearby Imperial River are a few examples. Teachers have been trained in implementing the Sunshine State Standards and effective teaching strategies, across the discipline area.

Gifted education students travel to the Everglades, Sea Camp in the Florida Keys and to the Cape Kennedy Space Center. Bonita Springs Middle School also works with the business community which supports the school's Renaissance Program.

All students are provided with an exploratory related arts program, consisting of Art, Business Technology Education, Computers, French, Spanish, Speech/Drama, and Band. Health and Physical Education are also key components to the students' educational experience.