The common bean (Phaseolus vulgaris L.) is an important crop that is often planted in areas that suffer from low water availability, leading to significant reductions in productivity. The breeding of genotypes better able to tolerate such conditions requires the efficient incorporation of resources present in germplasm banks. To this end, we investigated the responses of thirty bean genotypes to intermittent drought stress, with the aim of identifying biochemical markers for drought tolerance. The genotypes analyzed presented significant variability in both productivity and levels of soluble sugars, starch and amino acids under both irrigated and drought conditions. Moreover, we observed changes in the levels of these components under drought stress, providing information on the responses of the bean plants to this condition. Correlation analysis indicated a lack of relationship between components of the stem and productivity. On the other hand, levels of several components of the grain, including starch, total soluble sugars and amino acids were strongly positively correlated with productivity under drought and irrigated conditions, making these components potentially useful biochemical markers for the selection of genotypes for breeding programs. Principal components analysis also indicated the presence of a relationship between biochemical composition and productivity, but reinforced the fact that multiple mechanisms are responsible for explaining the differences in productivity between tolerant and susceptible genotypes.