Stunting predominantly occurs during the first 1000 days of life and continues to the age of five years. We will aim to assess the effectiveness of specialized nutritious foods (SNF)and social and behavior change communication (SBCC) strategies during the first 1000 days of life to prevent stunting among children in two rural districts of Badakhshan, Afghanistan. This will be a quasi-experimental pre-post study with the control group utilizing qualitative and quantitative methods. Before launching the program, formative research will be conducted on the acceptability, appropriate use and SBCC strategies needed to support the introduction of intervention package. Repeated cross-sectional baseline and endline surveys will be conducted in both the intervention and the control districts. After the formative research and baseline household survey, an intervention focusing on the provision of SNF, targeting pregnant and lactating women and children 6–23 months, and SBCC strategies will be implemented for at least 12 months. The primary outcome will be a reduction in the prevalence of stunting among children under two years in the intervention group compared to the control group. We will aim to compare the intervention and control group between the pre- and post-intervention assessments to isolate the effect of the intervention by difference-in-differences estimates. The program monitoring and evaluation component will examine the quality of implementation, acceptability of intervention, identification of potential barriers and to learn how to enhance the program’s effectiveness through ongoing operational improvements. The results will be beneficial to design interventions to prevent stunting within Afghanistan and other low–middle-income countries.