Knowledge of the uptake and fate of mercury (Hg) compounds in biota is important in understanding the global cycling of Hg and its transfer pathways through food chains. In this study, we analysed total mercury (T-Hg) and methylmercury (MeHg) concentrations in 117 livers of Scottish birds of prey that were found across Scotland and submitted for post-mortem examination through the Raptor Health Scotland project between 2009 and 2019. Statistical comparisons focussed on six species (barn owl, Tyto alba; Eurasian common buzzard, Buteo buteo; golden eagle, Aquila chrysaetos; hen harrier, Circus cyaneus; Eurasian sparrowhawk, Accipiter nisus; and tawny owl, Strix aluco) and showed that golden eagles had a statistically lower fraction of MeHg compared to other raptor species. Further investigation using stable carbon and stable nitrogen isotope ratio measurements carried out for the golden eagles (n = 15) indicated that the increased presence of inorganic mercury (iHg) correlated with a marine influence on the primarily terrestrial diet. Additional bioimaging (n = 1) with laser ablation – inductively coupled plasma – mass spectrometry indicated the co-location of Hg and selenium (Se) within the liver tissue and transmission electron microscopy showed evidence of nanoparticles within the range of 10–20 nm. Further analysis using single particle – inductively coupled plasma – mass spectrometry (n = 4) confirmed the presence of Hg nanoparticles. Together, the evidence suggests the presence of mercury selenide (HgSe) nanoparticles in the liver of some golden eagles that, to our knowledge, has never been directly observed in terrestrial birds of prey. This study points to two alternative hypotheses: these golden eagles may be efficient at breaking down MeHg and form HgSe nanoparticles as a detoxification mechanism (as previously observed in cetaceans), or some golden eagles with elevated iHg may have accumulated these nanoparticles by foraging on stranded cetaceans or seabirds.