Beneficial interactions between plant root exudates and the rhizosphere microbial community can alleviate the adverse effects of environmental stress on crop yields, but these interactions remain poorly understood in potato growing in drying soil. We investigated the responses of rhizosphere soil microorganisms and metabolites, and biochemical and physiological responses of two potato genotypes with contrasting drought tolerance (drought tolerant ‘C93’ and drought sensitive ‘Favorita’), to two different irrigation treatments imposing contrasting soil water availability in the field. Deficit irrigation altered rhizosphere soil bacterial communities and metabolites of C93 more than Favorita. While the abundance of Nitrosospira and Nitrobacter belonging to the Proteobacteria increased in C93, in Favorita the Streptomyces and Nocardioides belonging to the Actinobacteria increased. These microbial changes were significantly correlated with rhizosphere organic acid concentrations, with 3-phenyllactic acid increasing in C93, and citric acid increasing in Favorita. Although deficit irrigation restricted shoot growth of C93 at the tuber initiation stage (unlike Favorita), its specific root length was 41% greater than Favorita irrespective of irrigation treatment. Deficit irrigation significantly increased foliar chlorophyll and proline accumulation of both genotypes, with the latter 28% higher in Favorita. Independent of irrigation treatment, yield of the more vigorous C93 (producing 22 and 89% more shoot biomass under deficit and full irrigation respectively) was 84% higher than Favorita. It was concluded that different potato genotypes selectively recruit beneficial microorganisms by secreting different organic acids to alleviate the adverse effects of deficit irrigation.