Agriculture is a key activity in guarantying food security, one of the Sustainable Development Goals set by the UN Agenda 2030 for sustainable development. However, agriculture can be an environmental impacting activity when it is managed without attention towards its environmental efficiency. Thus, the assessment of eco-efficiency in agriculture is a crucial tool to evaluate this economic activity in terms of both natural resources exploitation and revenue generation. To address the complex issues associated with this problematic trade-off, the application of a Data Envelopment Analysis (DEA) has been to assess the environmental and economic performance of agriculture in terms of eco-efficiency. DEA has been applied the Italian case study at regional level, to provide policy-makers with a synthetic indicator of agricultural sustainability, when implementing funding policies. In particular, the analysis of the case study has taken into account the implementation of the European Common Agricultural Policy (CAP), as implemented through the Rural Development Plans. Our approach is a first step in the direction of assessing the long-lasting issue of developing benchmarking policies between the different Italian regions. This works paves the way to future and more in-depth studies needed to determine the eco-efficiency at local scale and, thus, the possibility to identify specific forms of agriculture as nature-based solutions.