Well-designed and managed marine protected areas (MPAs) can have positive outcomes for reef biodiversity, but their effectiveness for conservation outcomes is also influenced by local environmental and anthropogenic factors. To assess the importance of local factors on MPA effectiveness, we compared field-collected data on total reef fish biomass from 922 sites inside and outside a network of 49 MPAs across temperate Australia using modelled predictions of biomass based on local biogenic habitat, physical environment and anthropogenic factors. We found fish biomass was 34% greater in fully protected MPAs in temperate Australia than predicted if they were openly fished, whereas biomass in partially protected MPAs was equivalent to fished sites. Local biogenic habitat and physical environmental features significantly shaped shallow reef biomass across large spatial scales but their effects did not differ between fished and fully protected MPA sites, providing reassurance that regional habitat change inside and outside MPAs will not greatly affect relative effect sizes. These findings affirm the role of fishing in shaping fish biomass on shallow reefs across broad spatial scales and underscore the importance of strict protection from fishing. Strategic MPA design and management should consider local conditions to refine expectations, optimize fish biomass recovery and enhance conservation outcomes.