Climate change can facilitate emergence of zoonotic and wildlife diseases, by changing environmental suitability for hosts, ectoparasites, and pathogens. However, the connections between climatic variables and diseases remains equivocal. We compiled a systematic database for the prevalence of 121 pathogenic microbial taxa in birds and bats, including 11,801 observations from over 450,000 individuals across Europe and surrounding regions. Using a space-for-time-substitution approach, we modelled the potential connection of climatic variables on the prevalence of different taxa. The prevalence of viral and in particular bacterial taxa in birds (376 species) and bats (39 species) positively correlated with temperature, while rainfall showed negative and positive correlations with the prevalence of bacterial and viral taxa, respectively. The results suggest that our warming biosphere is subject to an emerging threat by pathogenic microbial taxa.