The systematic designation of protected areas is a key strategy in modern biodiversity conservation. As for now, the Natura 2000 system of the European Union (EU) is the largest coordinated network of conservation areas worldwide. Since this scheme has a focus on forests, its effectiveness substantially depends on small-scale private forest owners who represent the largest forest ownership group in Europe. We conducted a quantitative survey (n = 1671) in Northwest Germany focusing on the perceived importance of ecosystem services, the performance of management practices, nature conservation attitudes, as well as stand characteristics of small-scale private forest owners with and without Natura 2000 sites. Forest owners perceived regulating and cultural services as more important than provisioning ecosystem services while having a multifunctional perspective on their forest. Owners with Natura 2000 sites had a stronger focus on resource use and, with the exception of habitat-tree protection, did not perform conservation measures more frequently than those without. Moreover, we found more negative nature conservation attitudes among this ownership group. In conclusion, the Natura 2000 scheme needs to be more strongly adapted to the demands of small-scale private forest owners, for example by increasing profound participation and establishing a results-based incentive scheme for conservation measures. The perspectives of small-scale private forest owners have to be considered comprehensively to ensure the effective and sustainable implementation of the Natura 2000 conservation network.