Significance It has been unclear whether understanding how biodiversity is maintained requires us to study species interactions within and across trophic levels simultaneously. Achieving this task remains, however, challenging for practical and theoretical reasons. Here, integrating a simple but detailed experimental plant–pollinator community and a tractable mathematical framework, we show that biodiversity is strongly affected by species competitive interactions among plants and among pollinators, as well as the mutualistic effects between pollinators on plants. Furthermore, we show that experimentally preventing some species to interact can modify the rest of the interactions and affect idiosyncratically the probability of species persistence. These effects are only observable within the empirical evaluation and not with traditional simulation approaches.