Unprecedented climate change, pollutants and habitat alterations are causing abiotic stress across all plants and animals. Global increases in temperature, as well as decreases in pH in the ocean, have already caused microbiome dysbiosis in a range of species, and previously commensal microbes have turned pathogenic in response to extreme environmental conditions. This will have far-reaching consequences for host survival and associated ecosystem functions. However, host microbiomes may actually be the key to buffering these unprecedented environmental changes. The host microbiome contains massive genetic potential, and their vast numbers, high turnover, wide metabolic scope and short generation times may afford opportunities for faster acclimatisation and adaptation. Examples of this already exist, although responses are likely to be highly context-dependent. It is becoming increasingly clear that preservation of the microbiome is likely to be the key to maintaining healthy ecosystems in an uncertain future. However, there are still large knowledge gaps in almost every area, which need to be urgently addressed so we can apply conservation efforts in a judicious manner.