Recent evidence suggested that the development of gut microbiota during infancy influenced metabolic, immune, and endocrine pathways in humans. Dysbiosis was associated with impaired child growth and the later development of chronic non-communicable diseases. The Child Health And Microbiome Development Study–Pakistan (CHAMP) was conducted to assess gut microbiota development and its associated maternal, child, and demographic factors in malnutrition-endemic communities. A prospective cohort of 70 mother–infant pairs was recruited from District Swat and followed for two years. Data on demographics, healthcare, diet, feeding practices, child health, anthropometric measurements, dry blood spots, and fecal samples were collected at multiple time points. Ethical approval was obtained from Khyber Medical University, and the study was registered on ClinicalTrials.gov. The findings were expected to improve