There is growing interest in using the ecosystem services framework for environmental risk assessments of plant protection products (PPP). However, there is still a broad gap between most of the ecotoxicological endpoints used in PPP risk assessment and the evaluation of the risks and effects of PPP on ecosystem services. Here we propose a conceptual framework to link current and future knowledge on the ecotoxicological effects of PPP on biodiversity and ecological processes to their consequences on ecosystem functions and services. We first describe the main processes governing the relationships between biodiversity, ecological processes and ecosystem functions in response to effects of PPP. We define 12 main categories of ecosystem functions that could be directly linked with the ecological processes used as functional endpoints in investigations on the ecotoxicology of PPP. An exploration of perceptions on the possible links between these categories of ecosystem functions and groups of ecosystem services (by a panel scientific experts in various fields of environmental sciences) then finds that these direct and indirect linkages still need clarification. We illustrate how the proposed framework could be used on terrestrial microalgae and cyanobacteria to assess the potential effects of herbicides on ecosystem services. The framework proposed here uses a set of clearly-defined core categories of ecosystem functions and services, which should help identify which of them are effectively or potentially threatened by PPP. We argue that this framework could help harmonize and extend the scientific knowledge that informs decision-making and policy-making.