The main populations of several globally threatened bird species survive in Mediterranean agroecosystems. Consequently, a number of areas considered important for the conservation of these birds are currently protected by EU legislation. The European Common Agricultural Policy (CAP), conceived to increase agricultural production, has no restrictions in these protected areas, which creates a conflict between current agricultural policy and legislation on biodiversity conservation. Long-term monitoring of flagship bird species in a Mediterranean protected area shows significant population declines. Similar declines also affect common farmland bird species in others agricultural protected areas, confirming a failure of the EU Biodiversity Strategy. If Europeans want to conserve these landscapes and their biodiversity, the present conservation model should change in farmland areas. Solutions must involve the prohibition of agricultural intensification, and the implementation of sustainable farming practices different from current CAP subsidies.