Approximately 14% of the world’s coral reefs have been lost to anthropogenic pressures such as climate change, habitat destruction and overexploitation. No-take marine reserves (NTMRs) continue to be the only conservation tool that can be applied at scales relevant to the extent of the pressures. The Great Barrier Reef Marine Park (GBRMP) is a network of management zones allowing decreasing levels of human use, from virtually unrestricted fishing that includes trawling and netting, to no-take zones and no-entry zones. Whilst the effectiveness of the no-take zones has received regular attention, this is the first time we describe the effects of all six zones, including no-entry zones, on coral reef communities. We use a 20-year dataset collected by the Australian Institute of Marine Science (AIMS)’s Long Term Monitoring Program (LTMP) to investigate differences in fish and benthic assemblages throughout the GBRMP’s zones. No-entry zones had higher abundance of reef sharks when compared to the other zones. Furthermore, total fish biomass in no-entry zones ranged from approximately 1.5-fold higher than no-take zones to 2.3-fold higher than restricted-fishing zones. Biomass of fisheries target species showed a similar pattern, with no-entry zones supporting approximately 3-fold higher biomass than fished zones and 1.8-fold higher biomass than no-take zones, but values similar to those in Scientific Research Closed zones. Additionally, the biomass of grazing fishes was higher, and the biomass of most farming damselfishes was lower, in no-entry zones than all other zones. We discuss the habitat and community-level effect of zoning, propose our results as a line of evidence for concerning levels of poaching, weigh up the effects of reserve placement, and argue that, shifted baseline notwithstanding, no-entry zones may be the last bastion of coral reef reference conditions.