The primary classroom at MSA is multi-age for children ages 3 to 6. The third year is equivalent to "kindergarten," when the child is 5 and will be turning 6. This is a very important year that completes a three-year cycle. In this classroom, the child is able to advance at their own pace and will experience being the "learner" first (when they are 3 and 4 years old) and, later on in the cycle, the "teacher" (5 and 6 years old).

The classrooms are beautiful, bright, and transmit a sense of calm and order, which are qualities needed by the children to concentrate on their work and respect the work being done by others. Each primary classroom has one full-time Montessori-trained and certified lead teacher, as well as a full-time assistant, who work with the children from 8:30 a.m.–3:30 p.m. The children have two 3-hour blocks of uninterrupted work: one in the morning and one in the afternoon.