Major shifts in ecological dominance are one of the most conspicuous but poorly understood features of the fossil record. Here we examine one of the most prominent such shifts, the Ordovician shift from trilobite to brachiopod dominance of benthic ecosystems. Using an integrated database of high-resolution paleoecological samples and body size data, we show that while the average local richness and relative abundance of trilobites declined significantly through the Ordovician, the estimated standing biomass of trilobites, and by implication the amount of energy that they used, remained relatively invariant. This is attributable to an increase in the average body size of trilobite species in our data set, and especially to the widespread occurrence of the exceptionally large Middle–Late Ordovician trilobite genus Isotelus. Brachiopods increase in both mean body size and relative abundance throughout the Ordovician, so that estimates of brachiopod biomass and energetic use increase substantially between the Early and Late Ordovician. Although the data set includes a range of depositional environments, similar trends are observed in both shallow subtidal and deep subtidal settings. These results suggest that diversification of the Paleozoic Fauna did not come at the energetic expense of the Cambrian Fauna. The declining relative abundance of trilobites may reflect a combination of numerical dilution and the necessary energetic trade-offs between body size and abundance.