Avian trichomonosis, caused by the protozoan Trichomonas gallinae, affects bird-eating raptors worldwide. Raptors can develop trichomonosis by feeding on infected prey, particularly Rock Pigeons (Columba livia), which are a reservoir for T. gallinae. Raptors may be particularly vulnerable to T. gallinae infection in degraded habitats, where changes in resources may cause raptors to switch from foraging on native prey to synanthropic avian species such as Rock Pigeons. Golden Eagles (Aquila chrysaetos) typically forage on mammals; however, habitat across much of their range is experiencing degradation through changes in land use, climate, and human encroachment. In 2015, we examined the prevalence of T. gallinae infection in Golden Eagle nestlings across western North America and conducted an intensive study on factors associated with T. gallinae infection and trichomonosis in southwestern Idaho. We found T. gallinaeinfection in 13% (12/96) of eagle nestlings across 10 western states and in 41% (13/32) of nestlings in southwestern Idaho. At the Idaho site, the probability of T. gallinae infection increased as the proportion of Rock Pigeons in nestling diet increased. Nestlings with diets that consisted of ≥10% Rock Pigeons had a very high probability of T. gallinae infection. We compared historical (1971–81) and recent (2014–15) diet data and incidence of trichomonosis lesions of nestling eagles in Idaho and found that the proportion of Rock Pigeons in eagle diets was higher in recent versus historical periods, as was the proportion of eagle nestlings with trichomonosis lesions. Our results suggested that localized shifts in eagle diet that result from habitat degradation and loss of historical prey resources have the potential to affect Golden Eagle nestling survival and supported the hypothesis that land use change can alter biologic communities in a way that might have consequences for disease infection and host susceptibility.