Duru et al. (Agron Sustain Dev 35:1259-1281, 2015) highlighted a missing tool for studying and improving the performance of cropping systems in the transition to highly diversified agriculture. In response, this paper proposes a concept for designing, modeling, monitoring, and auditing desired ecosystem services, in intercropping and agroforestry systems. We have labelled this concept ESSU (Ecosystem Services functional Spatial Unit). It delimits the smallest spatial unit encompassing all the interacting species and other functional components (e.g., crops, trees, livestock, spontaneous vegetation, semi-natural habitats such as hedges, ditches, forest patches, and animals) that together provide a specified set of ecosystem services. The novel ESSU concept allows representation of an entire diversified agroecosystem by the repetition of the spatial unit that provides the same sets of targeted ecosystem services as the agroecosystem it represents. It can then be used for various activities, such as the (i) design of more efficient agroecological systems according to the targeted ecosystem services; (ii) rapid audit of farming practices for biodiversity/resilience across large tracts of farmland as part of achieving Sustainable Development Goal 2 targets of sustainable food systems; and (iii) modeling such diversified agroecosystems using a motif adapted to represent the targeted ecosystem services and the species spacing design. We demonstrate that the ESSU concept is highly flexible and applicable to a wide range of diversified agroecosystems, like arable intercropping, crop-tree intercropping, tree-tree agroforestry, and agro-pastoralism. We also show its relevance and suitability for representing temporal changes over 1 year, across several years, and over decades, indicating its generalizability and flexibility. We argue that ESSU could open new theoretical and practical research avenues for the study of diversified agroecosystems. Considered with all the knowledge available on practices, biodiversity, and ecosystem services, ESSU might provide a learning-support tool to fill the knowledge gap about relationships among practices, biodiversity, and associated ecosystem services.