Abstract Urban growth is a major threat to biodiversity conservation at the global scale. Its impacts are expected to be especially detrimental when it sprawls into the landscape and reaches sites of high conservation value due to the species and ecosystems they host, such as protected areas. I analyzed the degree of urbanization (i.e., urban cover and growth rate) from 2006 to 2015 in protected sites in the Natura 2000 network, which, according to the Habitats and Birds Directives, harbor species and habitats of high conservation concern in Europe. I used data on the degree of land imperviousness from COPERNICUS to calculate and compare urban covers and growth rates inside and outside Natura 2000. I also analyzed the relationships of urban cover and growth rates with a set of characteristics of Natura sites. Urban cover inside Natura 2000 was 10 times lower than outside (0.4% vs. 4%) throughout the European Union. However, the rates of urban growth were slightly higher inside than outside Natura 2000 (4.8% vs. 3.9%), which indicates an incipient urban sprawl inside the network. In general, Natura sites affected most by urbanization were those surrounded by densely populated areas (i.e., urban clusters) that had a low number of species or habitats of conservation concern, albeit some member states had high urban cover or growth rate or both in protected sites with a large number of species or habitats of high conservation value. Small Natura sites had more urban cover than large sites, but urban growth rates were highest in large Natura sites. Natura 2000 is protected against urbanization to some extent, but there is room for improvement. Member states must enact stricter legal protection and control law enforcement to halt urban sprawl into protected areas under the greatest pressure from urban sprawl (i.e., close to urban clusters). Such actions are particularly needed in Natura sites with high urban cover and growth rates and areas where urbanization is affecting small Natura sites of high conservation value, which are especially vulnerable and concentrated in the Mediterranean region.