Ticks are temporary ectoparasites that serve as vectors for a wide range of pathogens affecting both wildlife and humans. In Greece, research on the prevalence of tick-borne pathogens in wildlife is limited. This study investigates the presence of pathogens, including Anaplasma spp., Babesia spp., Bartonella spp., Rickettsia spp., as well as tick-borne encephalitis (TBE), and Crimean–Congo hemorrhagic fever (CCHF) viruses, in ticks collected from 28 wild animals across 10 different animal species. Ticks were manually harvested and identified using molecular methods, with sequencing confirming the presence of Hyalomma aegyptium, H. marginatum, H. anatolicum, Ixodes frontalis, and I. ventalloi. Among the pathogens detected, R. aeschlimannii was the most prevalent, particularly in H. aegyptium ticks from tortoises. Additionally, R. africae was identified in H. aegyptium from tortoises, marking the first report of this pathogen in this tick species in Greece. Hemolivia mauritanica, an apicomplexan parasite commonly found in Testudo tortoises, was also detected. No evidence of Babesia spp., Anaplasma spp., Bartonella spp., or viral nucleic acid was found. Phylogenetic analysis revealed close genetic relationships between the detected Rickettsia species and those previously reported in neighboring regions. These findings underscore the role of wildlife in the epidemiology of tick-borne pathogens in Greece and highlight the need for comprehensive surveillance to prevent future outbreaks.