<p>Phanerozoic marine biodiversity dynamics have been shaped by continuous environmental change and biotic interactions. Although ecosystem engineers – animals whose behaviours modify resource availability – have established impacts on modern community ecology and diversity, their impacts on ancient ecosystems over geologic time have remained quantitatively underexplored. Here, we investigate how biodiversity was impacted by reef-building or bioturbating ecosystem engineers at each stage of the Phanerozoic, including their ability to maintain biodiversity over mass extinctions, and identify extrinsic conditions that modulate their impacts. We analyse fossil communities with and without ecosystem engineers to calculate effect sizes, thereby quantifying the effects of the presence of ecosystem engineers on Shannon’s Diversity (<i>H</i>) at each stage in the Phanerozoic. We show that ecosystem engineers are significantly associated with increased biodiversity during the majority of the Phanerozoic. We also show that, over the last ~250 million years, the effectiveness of modern-type reef-builders is more sensitive to climate-driven stress than for modern-style bioturbators. Finally, our results reveal that climate may modulate ecosystem engineer impacts, with both bioturbators and reef-builders exhibiting the strongest effect sizes within an optimal moderate temperature range. These results underscore ecosystem engineers’ crucial role in contributing to fluctuating biodiversity dynamics over the Phanerozoic.</p>