Human–wildlife conflicts may have devastating consequences for fauna due to targeting by humans of wildlife populations suspected to have predated livestock. Suspicion of depredation of extensively raised livestock by vultures in Europe has triggered public administration-led forensic investigations intended to distinguish between predation and scavenging in order to compensate farmers for attacks on their livestock. In this study, gross and histological analyses were carried out on suspected cases of domestic animal depredation by griffon vultures (Gyps fulvus) over a 1-year period. Fifty-eight animals were affected (n = 41, suspected depredation), including domestic cattle (75.9%), sheep (22.4%) and a goat (1.7%). All the adults affected were female and most cases of suspected depredation occurred during the peripartum period (56%). Histological investigations distinguished between post-mortem (84% of diagnostic samples) and ante-mortem (16% of diagnostic samples) cases, and gross examinations revealed significant differences (P ≤ 0.002) between ante-mortem, post-mortem and non-diagnostic samples. This study highlights the need to optimize sampling protocols to increase the success of forensic studies. The forensic investigations presented here may be applied to resolve human–wildlife conflicts involving not only vultures but other endangered carnivores and contribute to human–wildlife coexistence in rural areas by protecting the interests of both the livestock sector and endangered species.