Seagrass roots host a diverse microbiome that is critical for both their growth and survival. However, the components driving the interplay between seagrasses and their associated root microbiome are still largely unknown. Using a multifarious approach combining imaging techniques (confocal fluorescence in situ hybridisation, oxygen planar optodes and sulphide DGTs), with plant physiology and molecular sequencing, we have now built a more complete picture of the micro-environment of growing roots of seagrasses. By using this approach, we reveal that both root exudates and root oxygen loss play an essential role in shaping the structure of the root microbiome. We highlight that seagrasses appear to ‘select’ for their microbiomes, and that these microbiomes confer adaptive advantages for their host in both nutrient acquisition and protection against pytotoxic sulphides in the sediment. We also highlight the importance of above-ground light availability for seagrasses in regulating the structure of their root microbiomes, where light reduction can invoke a cascade of changes from alterations in root exudation and oxygen loss to a reduction in putative beneficial microorganisms and, ultimately, confirms the importance of the seagrass root environment – a critical, but often overlooked space.