Intensive agricultural practices have increased world food production. However, this resulted to the accelerated environmental degradation, loss of biodiversity and destruction of ecosystem services upon which long-term resilience of food system depends. One of the possible solutions to have sustainable agricultural productivity versus environmental protection, climate resilience, and nutrition security in future is to includes Neglected and Underutilized Crops (NUCs) in the food system. This chapter provides information about potential of NUCs in improving ecosystem services and enhancing socio-ecological resilience to climate change and resource limitation. The chapter elaborates ecosystem services theory, and measures how the NUC-based diversification facilitates the provisioning, regulation, support, and cultural services through the improvement of soil health, water regulation, carbon sequestration, biodiversity conservation, and maintenance of traditional knowledge systems. It is also the role of NUCs in assisting the agroecosystems to resist climatic variability and environmental shock and providing processes of the ecosystem that are essential to long-term productivity. The chapter also discusses about the economic incentives and policy tools like the payment of ecosystem services, market-based tools and institutional underpinnings that can be used in favor of the wider use of NUCs and an assessment of critical financial, technical and governance constraints. The United States, South Asia and Sub-Saharan Africa case studies show that the practice of NUC cultivation can contribute to improving ecosystem services and livelihood in different environments. This chapter points to the importance of the inclusion of NUCs in the sustainable agricultural systems as a pillar of climate-sensitive, resilient, and ecosystem services-driven transformation of food systems in binding the environment protection, food and nutrition security, and policy innovation.