The wolf (Canis lupus) is used as a case study to rate Natura 2000 sites in Greece based on preferred wolf habitat characteristics and test whether the network is suitable for their conservation. Road density, agricultural area, site area, connectivity, food availability (i.e., presence of natural prey), and elevation in 237 sites are combined in a logistic regression model. The occurrence of the wolf's natural prey was the most prevalent factor determining wolf presence, followed by agricultural cover. Considering the current status of these features at N2K site level, most sites currently hosting wolves (85.7%) have good or excellent prospects for the long-term presence of the wolf. On the contrary, 11 sites which now have wolves are predicted to be ineffective in keeping them in the future due to the absence of wild ungulates and their high agricultural coverage. Four sites with no wolf presence currently have excellent prospects to host wolves in the future. Roadless sites are a priority for protection and retaining their current condition is strongly suggested. The proposed approach aims to detect gaps in protection for the wolf and identify priority sites in need of mitigation actions. It can also assist the assessment of conservation policies in Greece and elsewhere toward accomplishing set goals in protected areas. By focusing on wolf protection, we hope to increase agencies' attention to deal with conservation effectiveness, especially in cases like Greece, where a number of sites are insufficiently known and protected and management measures are not properly implemented.