Nutrition-sensitive agriculture (NSA) provides a promising pathway for addressing malnutrition. Fulfilling this promise needs a better understanding of the implementation and sustainability of NSA interventions because of their highly complex nature. This study aimed to explore the factors affecting the implementation and sustainability of NSA interventions. A case study design was employed using two focus group discussions with beneficiaries (n = 15), semi-structured interviews with beneficiaries (n = 13), and actors involved in implementation (n = 18). Factors were thematically analyzed using both deductive and inductive approaches adapting the consolidated framework for implementation research. A complex interaction of the factors across the five domains was found: outer setting—nutrition sensitivity of policies, institutional framework; inner setting—culture, social and economic environment, biophysical environment, local capacity, other programs or projects; characteristics of actors—beneficiaries, family members, household capacity, implementers; intervention characteristics—adaptability, design quality, cost of interventions; and, implementation process—fit-to-context, integration and multisectoral collaboration, continuous motivation through engagement, monitoring. Implementing and sustaining NSA needs consideration of multiple factors, with careful analysis of the absorptive capacities of local institutions and beneficiary households. Future studies should explore which mechanisms created for adoption can be continued beyond the project funding cycle, and how.