IntroductionEnvironmental and psychosocial adversities negatively impact children’s developmental outcomes. When these factors are experienced in early childhood—a sensitive period of development—the developing brain can be altered. While these associations have been drawn in high-income countries, it is necessary to understand child growth, neurodevelopment, and the role of environmental factors in developmental trajectories in low-income settings. The objective of this study is to longitudinally assess how demographic factors, maternal health, maternal development, and child health, are related to child development on a behavioural, cognitive, and neuroimaging level in low-socioeconomic communities.Methods and analysisMother–child dyads will be identified in the peri-urban field sites of Rehri Goth and Ibrahim Hyderi, Karachi, Pakistan. Dyads will undergo yearly assessments for 4 years beginning when the child is 1 month, 3 months or 6 months of age (+≤30 days of age) (depending on group assignment). Maternal assessments include anthropometry, behavioural, cognitive, and developmental assessments (Edinburgh Postnatal Depression Scale; Parenting Stress Index; Maternal Autonomy Index; Hurt, Insult, Threaten, Scream Tool; Reynolds Intellectual Assessment Scales (RIAS)), and biological samples collection (breast milk, blood, stool, hair). Children’s assessments include anthropometry, developmental assessments (Global Scales for Early Development (GSED); RIAS), MRI brain assessments, and biological sample collection (blood, stool, hair). Using cross-sectional and longitudinal data with statistical analysis tools, associations will be quantified between brain structure (MRI) and connectivity (resting state connectivity and diffusion tensor imaging), general cognitive skills (RIAS, GSED) and environmental influences (nutrition via biological samples, maternal mental health via questionnaires) through repeated measures analysis of variance tests and χ2tests. Quantile regression and cortical analyses will be conducted to understand how demographic factors are related to the associations found.Ethics and disseminationThe study has received ethical approval from the Aga Khan University Ethics Review Committee. The study’s findings will be disseminated through scientific publications and project summaries for the participants.