The implementation of the Free Public Education System and the improvement of transportation infrastructure resulted in a decline in enrollment.

In 1988, the Fund for Assistance to Private Education (FAPE) program was introduced, providing 1.5 million pesos in annual government aid.

On June 1, 2001, a fire destroyed the school's main building, including its administrative offices, library, faculty room, armory, reception area, and science laboratories.

The Securities and Exchange Commission (SEC) reissued MACI's registration on September 2, 2002, and in April 2003, the Department of Education and Culture granted the school its official certificate of recognition.

The school has also constructed a promenade, allowing students and visitors to access the nearby beachfront and coral reefs.