The development of sustainable agricultural systems in drylands is currently a crucial issue in the context of mitigating the outcomes of population growth under the conditions of climatic changes. The need to meet the growing demand for food, fodder, and fuel, together with the hazards due to climate change, requires cross-disciplinary studies of ways to increase livelihood while minimizing the impact on the environment. Practices of agroforestry systems, in which herbaceous species are intercropped between rows of woody species plantations, have been shown to mitigate several of the predicaments of climatic changes. Focusing on agroforestry in drylands, we address the question of how we can improve the performance of agroforestry systems in those areas. As vegetation in drylands tends to self-organize in various patterns, it seems essential to explore the various patterns that agroforestry systems tend to form and their impact on the performance of these systems in terms of biomass production, resilience to droughts, and water use efficiency. We use a two-soil-layers vegetation model to study the relationship between deep-rooted woody vegetation and shallow herbaceous vegetation, and explore how self-organization in different spatial patterns influences the performance of agroforestry systems. We focus on three generic classes of patterns, spots, gaps, and stripes, assess these patterns using common metrics for agroforestry systems, and examine their resilience to droughts. We show that in contrast to the widespread practice of planting the woody and herbaceous species in alternating rows, that is, in a stripe pattern, planting the woody species in hexagonal spot patterns may increase the system’s resilience to droughts. Furthermore, hexagonal spot patterns reduce the suppression of herbs growth by the woody vegetation, therefore maintaining higher crop yields. We conclude by discussing some limitations of this study and their significance.