BackgroundThis study aimed to investigate the association between inclusion to Pantawid Pamilyang Pilipino Program (4Ps), a CCT program in the Philippines, and malnutrition in children and adolescents and examine the perceptions and experiences of parents and other stakeholders on how 4Ps influenced child nutrition.MethodsA concurrent mixed-method study was conducted in the Caraga Region, Philippines. Quantitative data from 5541 children and adolescents aged 3 to 19 were analyzed using multilevel mixed-effect logistic models. To allow in-depth understanding of the programmatic components that support the findings from the quantitative study, eight focused group discussions (FGDs) were concurrently conducted, cumulating 33 participants, including 4Ps parents, school coordinators/teachers, and school nurses. A constructivist grounded theory approach was used for analysis, and joint displays were employed to integrate quantitative and qualitative results.ResultsQuantitative findings revealed high rates of malnutrition, with significant rates of stunting (12.0%), wasting/thinness (9.4%), and overweight/obesity (16.4%) among children and adolescents. 4Ps beneficiaries had higher odds of stunting and overweight/obesity compared to non-4Ps beneficiaries (AOR = 1.43, 95%CI: 1.08–1.91; AOR = 1.21, 95%CI: 1.01–1.45, respectively). However, no significant association was observed between inclusion to 4Ps and concurrent stunting and wasting/thinness or overweight/obesity (AOR = 1.05, 95%CI: 0.72–1.55). Geographic variations were observed, with 4Ps children in Agusan del Sur having lower odds of stunting than those in Agusan del Norte (AOR = 0.41, 95%CI: 0.23–0.71). Age and gender also showed significant associations with malnutrition. The qualitative analysis provided insights into the challenges contributing to malnutrition, including child labor, sickness, long distances to school, limited access to healthy food, and larger families. Unintended consequences such as cash card mismanagement, inappropriate cash grant allocation, and falsification of school attendance were identified. However, teachers and parents demonstrated resilience by implementing adaptive approaches to enhance child nutrition.ConclusionsWhile 4Ps beneficiaries exhibit higher odds of stunting and overweight/obesity, the program’s association with malnutrition was significantly influenced by geographic variations. It is crucial for social protection programs to prioritize comprehensive support strategies that effectively counter unintended consequences and challenges faced by beneficiaries and other stakeholders and address malnutrition in children and adolescents.