The legume-rhizobium interaction induces formation of specific reactions that take metabolism in the host plant up to a new functional level, increasing its tolerance to unfavourable cultivation conditions. Our objective was to study the participation of key enzymes – phenylalanine ammonia lyase, guaiacol peroxidase, and polyphenol oxidases – in the phenol-metabolism processes and synthesis of a broad spectrum of secondary metabolites in soybean plants that have established symbiotic interactions with rhizobia of varying effectiveness during optimal and insufficient water supplies. In our studies, we used symbiotic systems of soybean and rhizobia (Bradyrhizobium japonicum) that varied in efficiency and virulence. In the period of active nitrogen fixation by soybean, from the third-true-leaf stage until budding, we created different water-supply regimes for the plants, including optimal watering at the level of 60% of full field capacity (control) and insufficient, at the level of 30% (drought). When the soybean was flowering, we recovered the optimal level of water supply (resumed watering). In the studies, we employed microbiological, biochemical, and physiological approaches. We determined the specificity of how key enzymes of the phenol metabolism such as phenylalanine ammonia lyase, polyphenol oxidase and guaiacol peroxidase in the nodules, roots, and leaves of the soybean reacted to different levels of water supply, depending on the functional efficiency of the symbiotic system involving strains of B. japonicum, varying in effectiveness and virulence. In the effective soybean-rhizobium symbiosis, there occurred insignificant changes in the activity of phenol-metabolism enzymes in the nodules, roots, and leaves during drought and after action of the stress. This evidence is that in symbiosis with effective rhizobia B1-20, soybean could realize its own defensive systems that regulate optimal functioning of phenol metabolism in dehydration conditions. In the low-effective 107 and ineffective 604k symbiotic systems of soybean, there was observed unstable dynamics of the activity of enzymes in leaves and roots, manifested in intensification or inhibition of their activity levels during drought or post-stress period. This indicates malfunctioning of the processes associated with phenol metabolism in the soybean plants. We concluded that tolerance of legume-rhizobium symbiosis to water deprivation depends on mutual involvements of the both symbiotic partners – host plant and rhizobia, their ability to fully realize the defensive systems for activation of the key enzymatic complexes taking part in regulation of phenol metabolism in plants.