Avian malaria is a globally distributed vector-borne infectious disease caused by haemosporidian parasites capable of driving population declines and even species extinctions, posing major challenges for conservation biology. However, its occurrence in scavenger birds, particularly vulture species, remains poorly understood. We conducted active monitoring in northeastern and central Spain, collecting 383 blood samples from free-living birds of all age classes, including obligate (all European vultures) and facultative (red and black kites) scavenger species, to assess the occurrence of avian malaria parasites and identify their lineages using a nested-PCR protocol. Overall haemosporidian prevalence was 3.4% (13/383), with Leucocytozoon and Plasmodium detected at values of 2.3% and 1.6%, respectively. Among positive birds, Leucocytozoon spp. (69.2%) were more common than Plasmodium spp. (46.1%), including two co-infected individuals. Red kites, cinereous, bearded, and Egyptian vultures harbored both Plasmodium and Leucocytozoon, while black kites and griffon vultures only showed Plasmodium and Leucocytozoon, respectively. Black kites exhibited the highest haemosporidian prevalence (8.3%), followed by cinereous vultures (5.3%), red kites (4.8%), Egyptian (4.6%), bearded (1.9%), and griffon vultures (1.3%). Interestingly, we report 10 new host–parasite interactions and describe a novel Leucocytozoon lineage (lGYPBAR01) infecting all European vultures except the griffon vulture. We also detected Plasmodium relictum pSGS1 in an adult red kite, the first confirmed occurrence of this lineage in adults of the species. Our findings highlight a previously overlooked threat to avian scavengers and suggest that global warming may further facilitate the spread of haemosporidian-infected vectors, underscoring the urgent need for targeted conservation measures and further research into parasite dynamics in vulnerable wild populations.