Muslims accord a high premium on education, primarily that which obtains spiritual knowledge, and secondarily, generally beneficial knowledge. Historical accounts prove that education in Islam thrived in the Philippines well before the colonial period but became increasingly marginalized as succeeding education systems were institutionalized. In the new millennium, the Philippine government initiated a program of educational accommodation for Muslim and indigenous peoples. This paper elucidates the Department of Education’s Muslim Education Program and the Commission on Higher Education’s policy standards and guidelines for its baccalaureate program in Islamic Studies.