Anthropogenic conversion of natural habitats is the greatest threat to biodiversity and one of the primary reasons for establishing protected areas (PAs). Here, we show that PA establishment outpaced habitat conversion between 1993 and 2009 across all biomes and the majority (n = 567, 71.4%) of ecoregions globally. However, high historic rates of conversion meant that 447 (56.2%) ecoregions still exhibit a high ratio of conversion to protection, and of these, 127 (15.9%) experienced further increases in this ratio between 1993 and 2009. We identify 41 “crisis ecoregions” in 45 countries where recent habitat conversion is severe and PA coverage remains extremely low. While the recent growth in PAs is a notable conservation achievement, international conventions and associated finance mechanisms should prioritize areas where habitat is being lost rapidly relative to protection, such as the crisis ecoregions identified here.