Increasing plant productivity whilst minimising environmental impact is essential to achieve food security for the increasing human population. Nitrogen is the main limiting nutrient for plant production and legumes have developed the ability to interact with symbiotic bacteria (rhizobia), overcoming the lack of nitrogen availability in soil. In this mutualistic partnership, the rhizobia fix nitrogen from the air and supply it to the plant in exchange for carbon and amino-acid compounds. There are variations on the process efficiency outcomes depending on aspects such as the bacterial strain, soil type used and the environmental conditions. To evaluate the plant-soil-microbe continuum we characterised microbial communities in Medicago truncatula plants inoculated with different rhizobial strains in three UK soils that vary in physical and biological properties as well as nutrient availability. Remarkably, we found that the rhizobial strain can shape the composition of the endosphere, showing that symbiotic state can affect both microbial recruitment and nutrient uptake. We identified new microbes whose abundance is associated with more efficient symbiosis, opening up new possibilities for crop improvement. We also found that the efficiency of symbiosis is affected by the plant clock via LHY clock gene activity and have developed the mechanism for this by performing a nodule timecourse in continuous daylight conditions to analyse gene expression using RNAseq and found a set of nodule specific genes that oscillate with 24h rhythms. These results highlight the relevance of the plant’s metabolism and circadian rhythmicity in the optimisation of the legume-rhizobia symbiosis, and this is likely to impact whole endosphere shaping.