Abstract In coral reef conservation and management, the prevailing metric of reef health is percent coral cover, a measurement commonly used with the assumption that each unit of live coral tissue has equivalent ecological value. Here we show that the reproductive output of a coral population is not proportional to the cover of coral present. Instead, when compared to declining populations nearby, high cover coral populations produced up to four times more larvae per square centimeter of tissue, resulting in up to 200 times higher larval production per square meter of reef. Importantly, corals that produced more larvae did not produce smaller larvae, as predicted by resource allocation theory. Instead, higher fecundity corresponded to higher energetic lipid reserves in higher cover coral populations. In the wake of unprecedented global coral bleaching, our findings suggest that the largest reductions in coral reproduction may occur when corals are lost from previously healthy populations.