Maternal diet is an obvious factor that influences the chemical and microbiological makeup of human milk. Thus, the physicochemical composition of human milk (total protein, total fat, moisture, ash, pH, total soluble solids, and carbohydrate) from Filipino women with varied body mass indices (BMIs) and its correlation with the mother's diet and microbiological content (total plate count, Staphylococcus, lactic acid bacteria, and Bifidobacteria) were assessed at 0 to 4 months of lactation. Breast milk samples, sociodemographic data, and dietary recalls were gathered from 34 healthy breastfeeding Filipino women who were categorized based on their BMIs (underweight n=7; normal weight n=16; overweight n=11) using a cohort, semi-longitudinal study design. The physicochemical and microbial compositions of the milk samples were analyzed. All 34 lactating participants were interviewed three times each month for their 24-hour food recalls. Descriptive statistics were used to describe the study population, physicochemical and microbial characteristics of the milk samples, and the dietary intake of the participants. Pearson's Chi-square was utilized to determine the association between variables. The results show that the nutrient indexes for each weight classification throughout the four months were not significantly different from one another. Values for the physicochemical composition of the milk samples were generally highest in the first month and the lowest values were obtained in the fourth month. The crude fat content of the human milk was associated with the participants' fat intake, while the maternal dietary fat intake was related to the pH values of the milk samples. The physicochemical characteristics and selected cultivable microorganisms of the human milk showed that the total fat of the milk was linked with the count of Staphylococcus collected during the fourth month of lactation (p<0.05). The results suggest that maternal diet can shape the physicochemical quality of human milk, which may indirectly influence microorganisms present in it.