Background/Question/Methods Research on the relationship between trophic structure and resource availability has a long-standing tradition, but empirical observations reveal new insights. Studies from lakes undergoing phosphorus reductions have reported a surprising (“paradoxical”) relationship, in which plant (phytoplankton) biomass increases with decreasing phosphorus concentration, even though phosphorus is a limiting resource. This pattern is not consistent with most hypotheses for trophic structure, which predict that plant biomass increases or remains constant with increasing resource availability. Tentative hypotheses for this surprising pattern include declines in phytoplankton’s quality/edibility as food or increased predation by fish on zooplankton. However, these effects have rarely been evaluated. Here we attempted to identify the pathway causing a surprising relationship between phosphorus and trophic structure (-phosphorus, +phytoplankton biomass, -herbivorous zooplankton biomass, in short: –phosphorus, +P, -H) in a lake undergoing phosphorus control (L. Lugano, Switzerland and Italy) using monitoring data. We used a two-step analysis, in which we identified the main factors controlling trophic structure, defined as the herbivore-to-plant biomass ratio (H/P), and then examined the effects of phosphorus on these factors. Based on theory we initially considered four candidate factors: phytoplankton’s growth rate, phytoplankton’s carbon-to-phosphorus ratio, phytoplankton’s edibility (proportion of edible size), and fish abundance. In an alternative analysis, we used phytoplankton taxonomic composition as a proxy for food quality. Results/Conclusions The trophic structure (H/P) of the lake was not associated with any of the four initial candidate factors. However, trophic structure was associated with phytoplankton’s taxonomic composition. In particular, H/P was associated with an ordination axis representing the relative abundance of green algae (generally edible) versus cyanobacteria (generally inedible and potentially toxic), with H/P increasing and P biomass decreasing with increasing proportion of green algae. This axis was associated with phosphorus, with the proportion of green algae increasing with phosphorus. Therefore, the –phosphorus, +P, -H pattern was probably caused by an effect on phytoplankton’s quality, resulting in lower transfer between P and H at lower phosphorus concentrations. Although it is often believed that cyanobacteria and low trophic transfer are characteristic of highly-enriched lakes (eutrophy), this study shows that in some lakes this effect is enhanced by reductions to moderate phosphorus concentrations (mesotrophy). The results highlight the role of phytoplankton composition/quality in influencing trophic structure and suggest that phytoplankton’s food quality integrates a complex combination of traits, which may not be reduced to common proxies such as carbon-to-phosphorus ratio and proportion of edible size.