Facing the decline of biodiversity worldwide, the conservation of the remaining natural and semi-natural areas is fundamental. To do so, the concept of green infrastructure has gained attention recently. This case study presents the method developed to identify the green infrastructure in a cross-border, urbanized territory between Switzerland and France in the area of influence of the city of Geneva. The first part of the methodology consists of calculating and mapping the inputs aggregated in four pillars: (i) the distribution of habitats as well as the predicted distribution of hundreds of plant and animal species, (ii) the supply of five ecosystem services, (iii) the functional connectivity for three animal species and the light pollution and (iv) five indices of landscape’s structure. These inputs are then used to run a prioritization model to identify the areas with the highest ecological interest according to these weighted inputs. The cross-border situation of this case study had impacts on the way the input data were gathered and weighted and on the way the output was created to consider the expectations of the three main local authorities involved, without creating any legal obligations on the implementation of the green infrastructure. As a positive sign of the usefulness of these results, the resulting maps were immediately transferred to the land use planners in charge of developing ambitious visions of the “Grand Genève” territory for 2050 in alignment with 10 objectives of ecological transition as recently agreed and signed by local authorities. The method presented in this article is flexible and includes a broad description of biodiversity, supporting a reliable network of areas with high ecological values for conservation purposes and human well-being.