Organismal abundance tends to decline with increasing body size. Metabolic theory links this size structure with energy use and productivity, postulating a size–abundance slope of −0.75 that is invariant across environments. We tested the robustness of this relationship across gradients of protist species richness (1–6 species), temperature (15°C–25°C) and time. Using replicated microcosms, we provide an empirical test of how temperature and biodiversity jointly shape the cross-community scaling relationship (CCSR). While our results support the expected slope of −0.75, we also found interactive effects showing the relationship is not invariant. Warming altered abundance scaling with size depending on richness; in high-richness communities, temperature favoured small protists, steepening the CCSR slope. These context-dependent responses emerged over time, suggesting a role of size-dependent species interactions in shaping responses to environmental change. Our findings demonstrate that cross-community size scaling is not fixed but shifts dynamically with ecological context.