Sweet potato (Ipomoea batatas L.) is an important crop in the world, cultivated in temperate climates under low inputs. Drought changes the plant biomass allocation, together with the carbon and nitrogen isotopic composition (d13C and d15N), whose changes are faintly known in sweet potato crops. Here, we show the biomass allocation of eight sweet potato accessions submitted to drought during 3 months, using the d13C, d15N, carbon isotope discrimination (¿13C), total carbon (TC) and water use efficiency (WUE) traits. The tolerant accessions had improved WUE, with higher TPB and TC. Storage roots and shoots had a heavier d13C content under drought stress, with greater 13C fixation in roots. The ¿13C did not show a significant association with WUE. The d15N values indicated a generalised N reallocation between whole-plant organs under drought, as a physiological integrator of response to environmental stress. This information can aid the selection of traits to be used in sweet potato breeding programs, to adapt this crop to climate change.