Aim: This study aims to explore pediatric malnutrition through an integrated Preventive and Social Medicine (PSM) approach, focusing on the interplay of socioeconomic, microbial, and biochemical factors to identify key determinants and inform targeted interventions. Materials and Methods: A cross-sectional study was conducted among 100 children aged 6 months to 5 years in urban and semi-urban areas. Data were collected on socioeconomic status, anthropometric measurements, dietary practices, microbial diversity, and biochemical markers. Socioeconomic data were gathered using a structured questionnaire, while stool and blood samples were analyzed for microbial diversity and micronutrient levels. Nutritional status was assessed using Z-scores (WAZ, HAZ, WHZ) based on WHO standards. Data were analyzed using descriptive statistics, multivariable logistic regression, and structural equation modeling. Results: The study revealed that 40% of children belonged to low socioeconomic status, with 55% of parents having primary or no formal education. Stunting (mean HAZ: -1.8 ± 0.6) was more prevalent than wasting or underweight. Biochemical analysis indicated mild anemia (mean hemoglobin: 11.0 ± 1.5 g/dL) and micronutrient deficiencies. Microbial analysis showed moderate gut microbial diversity (Shannon Index: 3.0 ± 0.5), with Firmicutes (40.0%) and Bacteroides (30.0%) as dominant taxa. Suboptimal dietary diversity (<3 diversity score) was observed in 20% of children, and hygiene gaps such as lack of latrines (25%) were noted. Conclusion: Pediatric malnutrition results from interrelated socioeconomic, microbial, and biochemical factors. This study highlights the need for an integrated approach to address root causes and create sustainable interventions. By applying preventive and social medicine principles, tailored strategies can be developed to improve child health outcomes and break the cycle of malnutrition.