In the context of climate change, more frequent drought events and heatwaves predict a significant decrease in soybean yields. As the world's most widely grown legume crop, there's an urgent need to enhance its resilience to ensure productivity. Plants live with diverse microbial communities which profoundly affect multiple facets of host performance, but if and how host development impacts the assembly of microbial communities is poorly understood. Here we examined bacterial communities across soil, epiphytic and endophytic niches of leaves and roots. This study also explored how heat stress and water stress, alone or combined, impacted soybean microbial communities in relation with root morphology. To that aim, two soybean genotypes with contrasted root architectures were grown in the 4PMI high-throughput phenotyping platform during their vegetative stage, under various climate conditions. Conditions included control, heatwaves, water deficit, and combined heatwaves and water deficit. The results showed that combined stresses provoked a specific response that was not simply the sum of the effects of water deficit and heat stress. For example, an increase in the abundance of the beneficial bacterial taxa like actinobacteria in the root endosphere was only observed under combined stresses. Concerning the rhizoplane, there were more actinobacteria under water stress or combined stresses than under other climatic conditions. In the root endosphere, Xanthobacteraceae differentiated the two genotypes. We will discuss the putative link between bacterial communities in the different tissues of soybean and plant ability to resist to heat and water stresses. In conclusion, our results suggested that environmental conditions profoundly influenced plant microbiome assembly. This study holds significance for the development of future methodologies aimed at managing the microbiome and highlights the need to consider plant interactions with micro-organisms to understand and enhance its resilience to stress.