The concept of green infrastructure (GI) seeks to identify and prioritize areas of high ecological value for wildlife and people, to improve the integration of natural values in landscape planning decisions. In 2018, the canton of Geneva, Switzerland, established a roadmap for biodiversity conservation, which includes the operationalization of GI covering 30% of the territory by 2030. In this paper, we demonstrate a GI mapping framework in the canton of Geneva. Our approach is based on the combined assessment of three ‘pillars’, namely species’ distribution, landscape structure and connectivity, and ecosystem services, to optimize the allocation of conservation actions using the spatial prioritization software, Zonation. The identified priority conservation areas closely overlap existing natural reserves. Including the three pillars in the landscape prioritization should also improve adhesion to the GI idea, without undermining the protection of threatened species. With regards to land use planning, public and private land parcels with high values for GI may require specific incentives to maintain their desirable characteristics, as they are more likely to be degraded than areas with more building restrictions. Visualizing priority conservation areas in a spatially explicit manner will support decision-makers in Geneva to optimally allocate limited resources for ecosystem preservation.