Diversified farming systems, for example those that incorporate agroforestry elements, have been proposed as a solution that could maintain and improve multiple ecosystem services. However, habitat diversification in and around arable fields has complex and inconsistent effects on invertebrate crop pests and their natural enemies. This hinders the development of policy recommendations to promote the adoption of such management strategies for the provision of natural pest control services. Here, for the first time we conducted a trait-based approach to investigate the effect of farming system on plant, invertebrate herbivore and invertebrate natural enemy communities. We then evaluated this approach by comparing the results to those generated using a traditional taxonomic approach. At each of three working farms, we sampled within an agroforestry field (a diverse farming system comprising alleys of arable crops separated by tree rows), and within a paired non-diversified area of the farm (arable control field). Each of 96 sample points was sampled between eight and ten times, yielding 393,318 invertebrate specimens from 344 taxonomic groups. Diet specialization or granivory, lack of a pupal stage, and wing traits in invertebrates, along with late flowering, short flowering duration, creeping habit and perenniality in plants, were traits more strongly associated with agroforestry crop alleys than the arable control fields. We hypothesize that this is a result of reduced habitat disturbance and increased habitat complexity in the agroforestry system. Taxonomic richness and diversity were higher in the agroforestry crop alleys compared to the arable control fields, but these effects were stronger at lower trophic levels. However, functional trait diversity of natural enemies was significantly higher in the agroforestry crop alleys than the arable control fields, suggesting an improved level of biocontrol, which was not detected by traditional diversity metrics. Of eight key pest taxa, three were significantly suppressed in the agroforestry system, whilst two were more abundant, compared to the arable control fields. Trait-based approaches can provide a better mechanistic understanding of farming system effects on pests and their natural enemies, therefore we recommend their application and testing in future studies of diversified farming systems.