Conservation regulations are instrumental for effective nature preservation, but several compliance and implementation failures jeopardize the achievement of their objectives, with strong potential to erode their legitimacy. Understanding how such deficits impact on stakeholders' perceptions is a matter of concern in pursuing truly effective tools. Here, using as case study the heterogeneous implementation of EU sanitary regulations which allow livestock carcasses to be left in situ in the Iberian Peninsula, we evaluated how uneven implementation affects farmers' perceptions towards scavengers. We interviewed 109 farmers at the border between Spain, with designated Scavenger Feeding Zones (SFZs), and Portugal, where SFZs are still under way. We detected a deficit in the implementation of European sanitary regulation and a low knowledge of this legislation by farmers (10%), which led to marked differences between countries in the perception of farmers on scavengers. Despite being expected to benefit from SFZs, Spanish farmers valued scavengers worse than Portuguese farmers. This unexpected outcome would be mediated by ca. 95% of the Spanish farmers interviewed (n = 48) still using the carcass collection system set after the outbreak of the mad cow disease, instead of adopting the new rules allowing carcasses abandonment at SFZs. Contrastingly, ca. 28% of the Portuguese farmers (n = 61) left livestock carcasses in the field without official approval. Our results support the initial hypothesis of more positive perceptions of scavengers by farmers leaving livestock carcasses in situ, while warning against assuming effective implementation of sanitary regulations in reality. Worryingly, as illustrated by the negative perception of Spanish farmers towards vultures, these implementation failures could turn out to an emergent farmer-wildlife conflict, which can jeopardize scavenger conservation.