Agri-environmental measures are considered the main tool available to stop the loss of biodiversity associated with the intensification of agriculture. However, the question of whether or not they constitute an adequate tool to achieve this objective continues to be the subject of scientific debate. The evaluations carried out so far offer very variable results in this regard. In general, the measures are effective when their objective is the conservation of specific species in well-defined regions, but this effectiveness is usually less when their objectives are broader, such as the conservation of biodiversity in a country or region. Several reasons have been proposed to explain the limitations observed in order to improve the effectiveness of the measures. The most appropriate conservation measures in each case will depend on the landscape context, as well as the level of intensification of the agricultural system of interest. In intensive agricultural systems, with intermediate levels of landscape complexity, generic measures based on the reduction of the intensity of agricultural uses should be applied, and aimed at the maintenance of the ecosystem services that the organisms that they harbor. Complex agricultural systems require the maintenance of extensive traditional uses that guarantee the conservation of complex landscapes with high levels of biodiversity, in combination with specific measures for threatened species present in them. To this end, tools of the Common Agricultural Policy (CAP) could be used, such as conditionality or programs for areas of high natural value, as well as specific territorial planning measures aimed at promoting heterogeneity and connectivity in agricultural landscapes.