Renewable-energy and transport infrastructure can fragment habitats and weaken ecological connectivity when siting is addressed only at the project-permitting stage. Using Western Macedonia, Greece, with detailed application in the Regional Unit of Florina, this study develops a screening-level decision-support framework that links biodiversity-relevant spatial evidence to strategic planning priorities. The framework combines exclusion and evaluation criteria derived from policy and the literature, elicitation from 17 regional experts, and PROMETHEE ranking of five strategic directions under four scenarios. GIS overlays relate existing and planned energy and transport infrastructure to Natura 2000 sites, wildlife refuges, roadless areas, pelican-use areas and terrestrial corridor proxies for large mammals. The perceived baseline assigned a normalized weight of 0.69 to energy and 0.01 to reversibility. The stakeholder-mean framework redistributed weight toward protected areas (0.21), reversibility (0.19), energy (0.18) and ecological corridors (0.16). The leading strategic direction changed from investment (+0.50) under the baseline to tourism (+0.43) under the stakeholder-mean scenario, while the between-direction spread narrowed from approximately 1.10 to 0.27 in the highest-score scenario. GIS screening identified persistent conflict areas in western Voras, pelican movement routes linking Prespa with other wetlands and the Kleidi terrestrial corridor. The mapped distances of 0.93, 1.81 and 2.00 km are stakeholder-derived scenario assumptions, not universal ecological thresholds or species-response distances. The framework is intended for early strategic screening and stakeholder deliberation, followed by species-specific surveys, cumulative-impact assessment and field validation.