Protected areas are important for preventing biodiversity declines, yet indicators of species' trends in protected areas rarely include threatened species. We use data from the first national Threatened Species Index developed in Australia to report on trends for threatened and near-threatened birds inside and outside terrestrial and marine protected areas. We adopted the Living Planet Index to calculate trends for 39 bird taxa at 16,742 monitoring sites (11,539 inside and 5,203 outside PAs) between 1985 and 2016. At a continental scale, the overall decline in the national index was smaller inside protected areas (66% decrease in average population abundance) than outside (77%), although after 2000 declines were greater within (36%) versus outside (26%) protected areas. Five out of seven jurisdictions showed similar switching in patterns over time. Protected areas initially had a greater net positive effect on trends of more imperiled birds than less imperiled birds, but between 2000 and 2016 declines of the most imperiled birds were greater inside protected areas than outside. Our analyses suggest that the effectiveness of Australia's protected area network at improving trends in threatened species has weakened, and support the hypothesis that trends for terrestrial birds outside PAs might be improving due to increased conservation efforts on private land. Although this study represents the most comprehensive collation of threatened species population time series and trends ever for Australia, the number of monitoring sites inside PAs was double that outside PAs, even though on average, more than 70% of threatened bird distributions occur outside PAs, with important gaps in monitoring across space, time and taxa that need to be filled to fully understand the effectiveness of public and private conservation actions at a national level. The results underline the importance of active management plus monitoring to track and report on long-term trends across species.