Malnutrition is a public health concern in the Philippines that presents a complex issue mainly because of its multi-dimensional origin. Grounded on the UNICEF conceptual framework on the causes of malnutrition, the research investigates the relationship between poverty and practices of mothers with nutritional status of children below five years old in Cebu Province, Philippines. A total of 652 mothers were surveyed in two cohort groups. One group was an implementation site of the ECCD F1K Program while the other is the control group. In processing data, One-way ANOVA was applied to compare the two cohorts in terms of malnutrition while chi square test was done to understand relationships between profile of mothers, poverty, practices and child malnutrition. Level of significance to test differences and relationships among variables was set at p≤0.05. Findings suggest that short term impact of intensive health and nutrition programs did not reverse malnutrition. The occurrence of chronic malnutrition was significantly linked with practices of mothers (p=0.009); while acute malnutrition (p=0.030) and overnutrition (p=0.000) were significantly associated with poverty. An interplay of predisposing factors were noted to affect both the practices of mothers and poverty. These factors included the mother’s age (p=0.000) and number of children (p=0.000) for practices of mothers, while occupation (p=0.047), number of children (p=0.000), educational attainment (p=0.000) and age of mothers (p=0.000) were linked to poverty. In order to address malnutrition in the Philippines, there is a need to prioritize government programs that focused on the First 1000 days of the child with emphasis on adolescent sexual reproductive health, social behavior change communication, and equitable education opportunities for families.