Large marine protected areas (MPAs) will likely multiply worldwide to address accelerating biodiversity loss. Coral reefs are an especially at-risk ecosystem, but our understanding of whether and how large MPAs will benefit reef recovery from disturbances remains limited. Here, we evaluate how fishes influence coral reef recovery and if there are cascading trophic interactions in the fish community that influence recovery. We combine i) a meta-analysis of previous research evaluating how fishes affect coral reef succession, ii) field surveys of sharks, fishes, and benthic cover, and iii) a 2.5-year coral recruitment experiment of caged, uncaged, and partially caged settlement tiles in a remote and large MPA, in the Chagos Archipelago. In both our meta-analysis and field experiment, we found variable effects of fishes on coral recruitment with no overall significant effect, but strong control by fishes on the developing benthic communities, where fishes promote crustose coralline algae and reduce macroalgae. Within the Chagos, fishes had a positive effect on corals in protected microhabitats but a negative effect on exposed surfaces, leading to an overall neutral effect from fishes. Although mesopredatory fish abundance was negatively correlated with shark abundance, these top-down effects did not cascade down the food web through herbivores and corallivores to coral recruitment and benthic succession. Thus, our results suggest that within this large MPA, herbivores are important in limiting algae during recovery and there are compensatory responses to the loss of benthic feeding fishes and sharks, with implications for coral reef persistence in the face of global change.