An important set of ecosystem services (ESs) delivered by green infrastructure (GI) is based on habitats and species protection and enhancement, that is on maintaining and improving biodiversity. Indeed, the second objective of the European Biodiversity Strategy recommends that ecosystems and their services are maintained and enhanced by establishing GI and restoring at least a 15% of the ecosystems which show up significant decay. From this perspective, habitat fragmentation can be considered one the most outstanding causes of a decreasing attitude of GI towards the delivery of habitat-based ESs, since it weakens the capacity to deliver such services by undermining the networking potential of habitats. In this study, we propose a study concerning the Metropolitan City of Cagliari which includes seventeen municipalities into a unique system of metropolitan government. Sixteen Natura 2000 sites (N2Ss) are located in the City, which amount to about 30% of the metropolitan area. We propose a methodological approach to identify ecological corridors (ECs) between N2Ss, based on the prioritization of functional land patches related to their suitability to deliver ESs concerning biodiversity maintenance and enhancement. The methodology consists of two steps: i. identifying the most suitable patches to be included in ECs on the basis of their accessibility, that is, on their negative attitude towards contributing to landscape fragmentation; ii. assessing, through a discrete-choice-model, the ECs identified through point i in terms of their suitability to be included in a metropolitan GI, starting from the territorial taxonomy based on biodiversity characteristics connected to N2Ss, habitat suitability, and recreational and landscape potentials.