This study evaluates the implementation of the Mother Tongue-Based Multilingual Education (MTB-MLE) program. Using qualitative methods consisting of key informant interviews with former and current Department of Education officials and focus group discussions with teachers and parents, it looked into the program theory, service delivery and utilization, and program organization. An online survey was also conducted to determine the extent of implementation at the school level. Findings show the breadth of challenges faced by the program from conceptualization to execution. It had to deal with linguistic diversity in the classroom, which challenges the primary model of implementation that assumes that a child is exposed to only one mother tongue rather than several. Another important conceptual issue is the lack of understanding and wrong appreciation of the basic rationale of the program among school implementers and parents. In terms of implementation, the program has been hampered by procurement issues and the lack of designated funds for operational activities, forcing it to compete with other school needs to fund its activities.