The diet composition of breeding Eastern Imperial Eagles (Aquila heliaca) was analysed in Hungary between 2005 and 2017, and compared with two previously published datasets from the periods of 1982–1991 and 1992–2004. Altogether the distribution of 8543 prey items of 126 different species and 29 other taxa were analysed within a 36-years period. We found that the previously abundant Common Hamster (Cricetus cricetus) became marginal (7.42%), while European Sousliks (Spermophilus citellus) practically disappeared (0.03%) from the diet of Imperial Eagles. Small game species, like the Common Pheasant (Phasianus colchicus) and the Brown Hare (Lepus europaeus) composed a remarkable part of the diet (11.22% and 28.11% respectively), which raised some conflicts with hunters regionally and probably also contributed to the high prevalence of persecution incidents against the eagles. In parallel with the loss of traditional prey species, corvids (13.10%), pigeons (8.90%), waterbirds (6.83%), other rodents (6.71%), Roe Deers (Capreolus capreolus) (5.59%), raptors and owls (4.88%) became regularly detected prey species. The temporal changes of the main prey categories were analysed between 1998 and 2017, when the ratio of Hamster and Pheasant showed significant decrease (-27.29% and -6.38%, respectively). The ratio of Brown Hare also showed slight decrease (-3.98%), but the change was not significant. On the other hand, the ratio of corvids, waterbirds and Roe Deers within the diet showed significant increase (+18.20%, +6.25% and +5.39%, respectively). The observed flexibility in the foraging behaviour of Imperial Eagles greatly facilitate conservation efforts, as they seems to be able to utilize the most abundant prey sources, i.e. they were not depending solely from the status of any single specific prey source. However, eagles could only shift and survive in those regions, where their traditional preys decreased, if alternative species were available for them.