The increasing frequency of droughts and heatwaves associated with climate change represents a significant threat to global soybean production. In light of the crop's pivotal role in global food security, it is crucial to develop strategies to enhance its resilience to these stressors. The objective of this study was to investigate the impact of water and heat stresses on soybean growth, water uptake and mineral nutrition. Two soybean genotypes with distinct root architectures were cultivated in controlled conditions under a variety of stress scenarios, including optimal conditions, heatwaves, water stress, and a combination of both. A comprehensive analysis was conducted, encompassing morphological characteristics, water uptake, mineral composition, metabolome profiling, and root transcriptome sequencing. By integrating these data sets, we aimed to identify the relationships between structural traits (leaf area, root architecture, biomass) and functional attributes (water use efficiency, element uptake, metabolite accumulation, gene expression) in order to gain insight into the plant's response to stress. Our findings indicated that one genotype demonstrated a higher susceptibility to combined heat and water stress. The genotypic difference was primarily attributed to functional variations, particularly in water uptake and the content of specific elements within the roots. Our research has revealed that magnesium, calcium, nickel, sulphur, and sodium, which are known for their roles in osmoregulation, play a crucial role in the plant's response to stress. This multi-omics analysis provides valuable insights into how soybean can adapt to climate change. By understanding how root architecture, ionome, metabolome, and transcriptome interact under different stress conditions, we can identify key traits and mechanisms that contribute to soybean resilience. These findings can inform breeding efforts to develop soybean cultivars that are better equipped to withstand the challenges posed by a changing climate.