Row crop agriculture covers over 1.28 billion ha of land globally. Though extremely productive in terms of yield, annual cropping systems rely on external inputs of energy, nutrients and pesticides, leading to a suite of ecological consequences. This chapter focuses primarily on the opportunities and challenges associated with alley cropping practices involving overstorey nut crops as one element of the solution to address global needs for economically viable food production, while enhancing environmental services. The chapter examines the key challenges facing nut-based agroforestry systems, focusing on the genetic improvement of nut trees as well as the challenge of managing temporal and spatial tree and crop interactions. The chapter addresses orchard design and management, pest management in nut tree alley cropping and financial decision support tools. Finally, the chapter focuses on a number of case studies and looks ahead to future research trends in this area.