This century, aggregate climate risks will likely outpace the adaptive capacity of some species, rendering existing marine protected area (MPA) boundaries ineffective in the long-term. To better represent ecological reality, climate refugia, often defined by slower rates of warming or more stable conditions, should consider additional climate metrics over multi-decadal timescales. Here, we project six climate metrics across IPCC-AR6 emissions scenarios to identify multivariate climate refugia within Australia’s existing MPAs. MPAs in north-western and eastern Australia are projected to be the most exposed to aggregate climate risks throughout the century. Climate velocities consistently exceed 350 km/decade in parts of the north-west and Coral Sea, with some south-eastern MPAs >600 km/decade. Cumulative marine heatwave intensity is greatest in latitudes south of 28°S, diverging most notably from 2050 across scenarios. While low emissions scenarios suggest that many refugia will be retained until 2100, scenarios consistent with current emissions reductions commitments indicate a nationwide disappearance of thermal refugia during 2041-2060. Our findings confirm that a substantial proportion of Australia’s MPAs lack long-term climate resilience, suggesting a reconfiguration of MPAs to a climate-smart network might be needed to conserve marine biodiversity in an increasingly warmer, acidified, deoxygenated ocean.