Marine protected areas (MPAs) provide biodiversity conservation benefits in a range of marine habitats. Many protected areas are established and governed through top-down or shared governance arrangements, yet little is known about how these governance strategies compare in terms of the protection benefits they provide to MPAs globally. Using an extensive data set of MPA conditions, we developed a set of Bayesian hierarchical models to understand the role of shared governance versus federal governance on reef fish biomass from 218 global MPAs. We find greater reef fish biomass benefits in MPAs with shared governance than with top-down, or federal arrangements. We also find greater benefits in older MPAs and MPAs farther away from shore. Our results highlight the fundamental importance of multi-stakeholder participation for improving conservation outcomes, representing an important conservation opportunity for new or existing MPAs.