Global climate change has been shown to cause variable shifts in phenology in a variety of animals and unexpected outcomes across food chains are to be found. Here we examined how rising annual spring temperatures affected the interactions between seed masting, cavity nesting birds and dormice using long-term data from Eastern Czech Republic. We have shown that climate change was associated with unequal shifts in the phenology of two cavity-breeding groups: dormice and birds. Rising spring temperatures have progressively advanced the termination of hibernation for the edible dormouse Glis glis, a common bird predator, leading to an increasing overlap in the use of nesting boxes between dormice and birds. In contrast, only the collared flycatcher Ficedula albicollis, of the four cavity-nesting bird species, advanced its breeding dates in response to rising temperatures. At the same time, favourable weather conditions, coupled with good seed masting years, have been associated with a substantial rise in dormice numbers. Concurrent with the increasing dormice abundance, the number of bird nests destroyed significantly increased in three out of four bird species. We showed that while there was a significant change in the date that the dormice emerged from hibernation during the course of the study, it did not significantly contribute to predation levels when controlling for their abundance and timing of breeding in birds. We found that the increasing dormice abundance was the main factor causing high brood losses in birds, while the timing of breeding in birds had a variable effect between bird species. This study illustrates how changes in climate might affect organisms at various trophic levels with often unexpected outcomes. Limited evidence from other study organisms suggests that species most at risk are those at different trophic levels that do not shift at the same rate or in the same direction as their food resources, predators or competitors.