The Natura 2000 (N2K) network combines biodiversity protection and socioeconomic targets. Human activities, such as agricultural practices, can affect biodiversity in N2K sites in diverse ways. Limiting activities with negative impacts while enforcing land management that supports biodiversity is crucial for effective conservation. Yet, site-level information on how this is addressed in N2K sites is lacking. To fill this knowledge gap, we conducted a European Union-wide survey among N2K site managers. We aimed to assess the implemented conservation measures, their funding sources, and the extent to which different threats are addressed. Of the 341 responses, 61.8% reported the implementation of conservation measures linked to agricultural practices, such as adapting mowing and grazing at levels suitable for the conservation of grassland habitats and species. Sites with management tied to agricultural practices relied more on EU funding, such as the Common Agricultural Policy (CAP), whereas other sites depended more on national funding. Threats not addressed by conservation measures were reported by 63.8% of respondents, suggesting that overall management funding may be insufficient or ineffectively allocated. Most of these unaddressed threats resulted from intensive agricultural practices, such as the use of agrochemicals (reported as a threat in 13% of sites). These findings provide insight into how traditional agricultural practices, mostly related to low-intensity grazing and mowing, are frequently used as conservation tools, whereas intensive agriculture is a prominent source of unmitigated threats. Thus, achieving N2K conservation goals requires avoiding intensive agricultural practices and strengthening effective conservation measures in protected areas.