Efforts have been made in Europe to support the adoption of agri-environmental measures (AEMs), with the ambition to combine both high standards of crop productivity and environmental quality. However, benefits from AEMs have been poorly quantified at the spatial scale, despite the increasing demand for a spatial-targeting approach that link site- specific payments with AEMs performance. The aim of this work was to develop an integrated model-GIS platform that was used as decision support system to evaluate best AEMs in terms of agronomic performance and agro-ecosystem quality. The study site was the Veneto Region, where the AEMs were applied from 2007 to 2013 according to the Rural Development Programme. Results showed that in general the continuous soil cover yielded both agronomic benefits and the improvement of environmental quality, while a change from mineral to organic fertilizations was effective in the long-term and in the loose soils of southern and western Veneto, improving the soil-water balance and the nutrients availability to the crops. These estimates provide a good starting point for decision-makers aiming to implement a spatial targeting approach that effectively evaluate the ecological effectiveness of agri-environmental policies.