Exposure to persistent organic pollutants (POPs), such as organochlorines (OCs) and polybrominated diphenyl ethers (PBDEs), is associated with adverse health effects in wildlife. Many POPs have been banned and consequently their environmental concentrations have declined. To assess both temporal trends of POPs and their detrimental impacts, raptors are extensively used as biomonitors due to their high food web position and high contaminant levels. White-tailed eagles (WTEs; Haliaeetus albicilla) in the Baltic ecosystem represent a sentinel species of environmental pollution, as they have suffered population declines due to reproductive failure caused by severe exposure to dichlorodiphenyltrichloroethane (DDT) and polychlorinated biphenyls (PCB) during the 1960s through 1980s. However, there is a lack of long-term studies that cover a wide range of environmental contaminants and their effects at the individual level. In this study, we used 135 pooled samples of shed body feathers collected in 1968–2012 from breeding WTE pairs in Sweden. Feathers constitute a temporal archive for substances incorporated into the feather during growth, including corticosterone, which is the primary avian glucocorticoid and a stress-associated hormone. Here, we analysed the WTE feather pools to investigate annual variations in feather corticosterone (fCORT), POPs (OCs and PBDEs), and stable carbon and nitrogen isotopes (SIs; dietary proxies). We examined whether the expected fluctuations in POPs affected fCORT (8–94 pg. mm⁻¹) in the WTE pairs. Despite clear temporal declining trends in POP concentrations (p < 0.01), we found no significant associations between fCORT and POPs or SIs (p > 0.05 in all cases). Our results do not support fCORT as a relevant biomarker of contaminant-mediated effects in WTEs despite studying a highly contaminated population. However, although not detecting a relationship between fCORT, POP contamination and diet, fCORT represents a non-destructive and retrospective assessment of long-term stress physiology in wild raptors otherwise not readily available.