Very young children thrive in the safe, structured, Christ-centered atmosphere at The Atonement Academy. They are encouraged to work hard and develop self-discipline, and they also learn to cooperate with each other and make friends. Young scholars focus on acclerated reading and math skills as well as phonics and music.

The lower school curriculum consists of Religion, Mathematics, English Language Arts (including Reading, Phonics, Grammar, Composition, Spelling, Vocabulary, and Penmanship), History or Social Studies, Science, Music, Athletics and Spanish. Students in fourth and fifth grade study Geography. Art classes may be offered at some grade levels. Proficiency in reading is emphasized because it is essential to all other studies; consequently, every student participates in the Accelerated Reader program.

Musical excellence is a hallmark of The Atonement Academy. Every Atonement scholar takes a full credit course in choral music every year. Each student is assigned to one of the academy's ten choirs. Choirs in Grades 3 through 12 take turns singing at the daily school Mass. Every choir performs at least twice yearly, in some cases more frequently. Our most proficient choirs are competitive state-wide. Every student is expected to participate fully in the music program.