Purpose: The purpose of the paper is to explore the implementation of Madrasah Education Program (MEP) in selected Arabic Language and Islamic Values Education (ALIVE) schools in Quezon City, Philippines and identify some challenges faced in their implementation practice. Design/methodology/approach: This study utilized qualitative method of research using exploratory study, employing in-depth interviews, document analysis, and observation. The authors used purposive sampling with eight research participants: one Administrator, three ALIVE Coordinators, and four Madrasah Teachers or Asatidz. Findings: The main findings in the MEP implementation, generally, the schools delivered some program goals through institutional support, pedagogical and instructional development, and enrichment of cultural diversity in the school community. However, the study identified some major challenges affecting the program implementation in selected ALIVE schools such as: lack of permanent infrastructure, limited instructional resources, learners' absenteeism, low and delayed Asatidz allowances, and cultural variances among Muslim Filipinos. Research limitations/implications: The results of the study provide a general overview of MEP implementation and the major challenges experienced by program implementers. However, the study is limited to three selected ALIVE schools in the Philippines. Practical implications: These results are useful in guiding education stakeholders in evidence-based policymaking to further improve the implementation of Madrasah Education. Originality/value: This study provides enrichment of evidence-based research especially on the lived experiences of grassroots implementers. Fewer studies on Madrasah Education were conducted outside the Bangsamoro Autonomous Region (BARMM) particularly in the context of a non-Muslim dominated locale.