Abstract Background Nutrition-sensitive interventions such as homestead production of diverse, nutrient-rich foods, coupled with behavior change communication, may have positive effects on the nutritional status and health of rural households engaged in agriculture, particularly among women and young children. Engagement of agriculture and health extension workers in these communities may be an effective way of delivering nutrition-sensitive interventions given the dearth of trained health care providers in many developing countries. This study aims to assess the effects of integrated homestead food production, food consumption and women’s empowerment interventions using a multi-sectoral approach on women’s and child’s health and nutrition. Methods This is a cluster-randomized community-based prospective study set in Rufiji district, a rural area in Eastern Tanzania. Ten randomly selected villages within the Rufiji Health and Demographic Surveillance Site (HDSS) in Eastern-Tanzania were paired and randomly assigned to the intervention or control arm. The Rufiji HDSS dataset was used to randomly sample households with women of reproductive age and children 6–36 months. The intervention includes provision of small agricultural inputs, garden training support, and nutrition and health counseling. This is delivered by community health workers and agriculture extension workers through home visits and farmer field schools. There are three time points for data collection: baseline, midline, and endline. Primary outcomes are women’s and children’s dietary diversity, maternal and child anemia status and growth (child stunting, child wasting, women’s BMI, and women and child hemoglobin). Discussion This integrated agriculture and nutrition intervention among rural farming households is a simple and innovative solution that may contribute to the reduction of undernutrition and disease burden among women and children in developing countries. Engaging already existing workforce in the community may facilitate sustainability of the intervention package. Trial registration ClinicalTrials.gov NCT03311698, Retrospectively registered on October 17, 2017.