The effect of climate change on flora and fauna has been widely discussed for years. However, its consequences on microorganisms are generally poorly considered. The main effect of climate change on microbiota is related to biodiversity changes in different regions of the planet, mainly due to variations in temperature. These alterations are resulting in a worldwide (re)distribution of pathogens, which was not considered a few years ago. They mainly affect different food chain sectors (such as agriculture, livestock and fishing), as well as human health. Hence, the spread of numerous animal and plant pathogens has been observed in recent years from south to north (especially in America, Europe and Asia), leading to the spread of numerous plant and animal diseases, which results in economic and ecological losses. In addition, global warming that accompanies climate change could also be related to emerging antibiotic resistance. However, the mitigation of climate change goes hand in hand with microorganisms, which can help us through different natural and industrial processes. Thus, this manuscript presents the direct and indirect effects of climate change on microorganisms described up to date and how they act on this worldwide phenomenon.