Conservation policies increasingly rely on multispecies indicators to track biodiversity change and evaluate conservation measures, yet the commonly used two-step indicators weight species equally and underestimate uncertainty. We propose a multispecies index estimated in a single step directly from raw site-level counts, transferable to any monitoring programme based on such data. We demonstrate it using 25 years (2000–2024) of Common Breeding Bird Survey data from Poland, comparing three species groups (all common, farmland and forest) inside and outside Natura 2000 Special Protection Areas (PAs), which cover 16% of the country. Abundance of all common species was 11% higher inside PAs over the study period, while farmland species were 11% less and forest species 33% more numerous inside PAs. During the first years of the study, bird numbers increased both inside and outside PAs, but faster within them (e.g. 5.4% vs 3.0% per year for all common species). In all groups, the trend reversed to decline or stabilisation earlier inside PAs: by 4.3 years in all common species, 6.9 years in forest birds and 2.0 years (not significant) in farmland birds. After this changepoint, rates of change stabilised inside PAs, while declines continued outside. These patterns suggest that high-quality habitats both reveal population change earlier and buffer subsequent declines. Protected areas are therefore not only important for conservation but also valuable as early indicators of population change, and indicators reported separately for protected areas could strengthen the monitoring of EU biodiversity targets.