Many butterfly populations respond negatively to land-use intensification in human-dominated landscapes. Networks of protected sites have been established with the aim to halt species loss. We undertook annual surveys of all occurrence sites of 22 uncommon butterfly species in eastern Denmark during the period 2014–2019 and compared to a systematic atlas survey done 1989–1993, in order to assess trends in regional occupancy of species. Three out of 22 species went regionally extinct between 1993 and 2015. One species sustained a single population through the study period. Logistic regression for the remaining 18 species showed 10 to be in strong decline from 1993 to 2015, two showed a declining trend and six had stable trends. For all species except one, the declining trend continued 2015–2019. For five species, a sustained strong decline was evident. In 1993, the total count of occurrence sites for all 22 butterfly species was 565, which by 2019 had declined to 158 sites (a 72 % loss over 26 years). From 2015 to 2019 alone, the total count of occurrence sites shrank from 200 to 158 (a 21 % decline over just four years). Legal protection of areas (Natura 2000 and Danish Nature Protection Act §3) was, unexpectedly, not associated with lower probability of local extinction for butterfly population. The observed sustained decline across species suggests an overall low efficiency of the network of protected sites, probably due to a combination of misguided management regimes and payment of extinction debts from the past.