<p>Plant diseases pose a great risk to global food security, and recent research indicates that pathogen pressures on plant productivity will substantially increase under ongoing climate change (that is, increasing CO₂ levels and global warming). However, our mechanistic and predictive knowledge of the impacts of climate extremes, such as heatwaves and prolonged droughts, and their interaction with other climatic factors, on plant pathogens, hosts and microbiomes, remains largely unknown. This is an important knowledge gap that limits our ability to develop effective strategies to mitigate the socioeconomic impacts of climate change-induced plant disease outbreaks. This Review examines the impacts of key climate extremes on soil-borne pathogens, plant microbiomes and host physiology that ultimately determine disease outcomes. We explore evidence that suggests that the responses of pathogen–host–microbiome interactions to climate extremes may differ in many ways from those to long-term climate change. Climate extremes may increase the virulence and distribution of many pathogens, suppress certain plant immune responses, and weaken the core functions of host microbiomes within the disease triangle, thereby facilitating disease outbreaks. We propose an integrated pathway for harnessing microbiomes to address the critical challenges posed by climate extremes. These insights offer new approaches to mitigate disease risks by harnessing microbiomes and metabolites under climate extremes, with the potential to support climate-resilient and sustainable agricultural and natural ecosystems.</p>