Childhood malnutrition is a global public health issue with devastating consequences on the health, well-being, and psychosocial development of children. Emerging evidence suggests that malnourished children have immature gut microbiota compared to age-matched healthy controls and it does not repair even after nutritional interventions. The present study aims to characterize how the gut microbiome develops during the first two years of life in children residing in malnutrition endemic areas of Khyber Pakhtunkhwa, the region with the highest prevalence of childhood malnutrition in Pakistan and the region.