High School MSAs provide Muslim students the opportunity to come together in a supportive Islamic environment in order to explore and understand Islam. It seeks to educate and increase awareness of students about Muslims and Islam around the world. The MYC nurtures the MSAs at each high school in the greater Raleigh area by providing guidance and support.

College MSAs run more independently from the MYC than the high school MSAs in that the MYC is not directly involved with the college MSA day-to-day activities. However the MYC helps to build the bond amongst all the university MSAs by fostering their relationship.