Studies of herbivores and secondary consumer communities rarely incorporate a comprehensive characterization of primary producer trait variation, thus limiting our understanding of how plants mediate community assembly of consumers. We took advantage of recent technological developments for efficient generation of phytochemical, microbial and genomic data to characterize individual alfalfa plants (Medicago sativa; Fabaceae) growing in an old‐field, semi‐naturalized state for 770 traits (including 753 chemical features). Using random forest modelling, we investigated the effect of variation in these traits on arthropod and fungal assemblages while accounting for plant genetic structure. We found that traits indicative of plant vigour, including size, percentage of flowering stems and leaf area, were positively associated with arthropod richness and abundance. Most phytochemicals were, by comparison, poor predictors, although phytochemical diversity and several individual phenolic compounds were important. Plants with a higher proportion of flowering stems were hotspots of intertrophic interactions with higher species richness of secondary consumers. The effects of many traits on plant‐associated assemblages were best modelled as nonlinear functions, often incorporating threshold effects. Foliar fungal richness was not well predicted by our models, suggesting we have much to learn regarding the role of plant traits on phyllosphere fungi at small spatial scales. Our results support the need for characterization of multiple axes of plant phenotypes in studies of plant‐arthropod‐microbe communities and demonstrate the value of modern analytical techniques for understanding the nonlinear ways in which plant traits mediate the structure of associated biotic communities. Aplain language summaryis available for this article.

An increasing number of ecological studies have used chemical diversity as a functionally relevant, scalable measure of phytochemical mixtures, demanding more rigorous attention to how chemical diversity is estimated. Most studies have focused on the composition of phytochemical mixtures and have largely ignored structural concerns, which may have greater importance for ecological function. Here, we explore the development of structural complexity and compositional diversity resulting from different biotic and abiotic interactions in Piper kelleyi Tepe (Piperaceae). We also describe how variation in structural complexity and compositional diversity differs between two congeners, P. kelleyi and P. reticulatum. To better interpret these results, we have developed a framework for interpreting these dimensions of chemical diversity in phytochemical mixtures. We used the tropical shrub, P. kelleyi, as a model system to examine interactions between ecological factors and dimensions of phytochemical diversity. We also compared compositional diversity and metabolic complexity in P. kelleyi and P. reticulatum using liquid chromatography and ¹H NMR, respectively, to examine trade‐offs between compositional diversity and structural complexity. A framework is provided to generate meaningful estimates of the structural complexity of phytochemical mixtures as measured by ¹H NMR. Piper is an abundant plant genus that supports diverse insect communities throughout the tropics. Subtle changes in understorey forest light were associated with increases in herbivory that directly increased compositional diversity and indirectly decreased structural complexity in P. kelleyi. This was attributed to the production of oxidation products resulting from herbivory‐driven decomposition of structurally complex defence compounds. This type of complex result would remain undetected using standard chemical ecology approaches and accounts for the detailed molecular changes that are likely to affect species interactions. Synthesis. Our quantitative framework provides a method for considering trade‐offs between structural complexity and compositional diversity and the interpretation of analytical approaches for each. This methodology will provide new theoretical insights and a more sophisticated model for examining the ecology and evolution of chemically mediated interactions.