Understanding how biotic interactions shape ecosystems and impact their functioning, resilience and biodiversity has been a sustained research priority in ecology. Yet, traditional assessments of ecological complexity typically focus on species-species interactions that mediate a particular function (e.g., pollination), overlooking both the synergistic effect that multiple functions might develop as well as the resulting species-function participation patterns that emerge in ecosystems that harbor multiple ecological functions. Here we propose a mathematical framework that integrates various types of biotic interactions observed between different species. Its application to recently collected data of an islet ecosystem—reporting 1537 interactions between 691 plants, animals and fungi across six different functions (pollination, herbivory, seed dispersal, decomposition, nutrient uptake, and fungal pathogenicity)—unveils a non-random, nested structure in the way plant species participate across different functions. The framework further allows us to identify a ranking of species and functions, where woody shrubs and fungal decomposition emerge as keystone actors whose removal have a larger-than-random effect on secondary extinctions. The dual insight—from species and functional perspectives—offered by the framework opens the door to a richer quantification of ecosystem complexity and to better calibrate the influence of multifunctionality on ecosystem functioning and biodiversity.