Research linking biodiversity and ecosystem functioning (BEF) has been mostly centred on the influence of species richness on ecosystem functions in small‐scale experiments with single trophic levels. In natural ecosystems, many ecosystem functions are mediated by interactions between plants and animals, such as pollination and seed dispersal by animals, for which BEF relationships are little understood. Largely disconnected from BEF research, network ecology has examined the structural diversity of complex ecological networks of interacting species. Here, we provide an overview of the most important concepts in BEF and ecological network research and exemplify their applicability to natural ecosystems with examples from pollination and seed‐dispersal studies. In a synthesis, we connect the structural approaches of network analysis with the trait‐based approaches of BEF research and propose a conceptual trait‐based model for understanding BEF relationships of plant–animal interactions in natural ecosystems. The model describes the sequential processes that determine the BEF relationship, i.e. the responses of species to environmental filters, the matching of species in ecological networks and the functionality of species in terms of their quantitative and qualitative contributions to plant demography and ecosystem functioning. We illustrate this conceptual integration with examples from mutualistic interactions and highlight its value for predicting the consequences of biodiversity loss for multispecies interactions and ecosystem functions. We foresee that a better integration between BEF and network research will improve our mechanistic understanding of how biodiversity relates to the functioning of natural ecosystems. Our conceptual model is a step towards this integration between structural and functional biodiversity research.