Cassava production faces challenges in a changing climate. Pulse labelling cassava with C-CO has the potential to elucidate carbon allocation mechanisms of cassava under drought stress and with potassium application. Understanding these mechanisms could guide efforts to mitigate effects of drought in cassava cropping systems. Forty-eight cassava plants received a nutrient solution high or low in potassium. Water deficit was imposed on half of the plants at bulk root initiation stage, after which they were labelled for 8 h with C-CO in a 15 m growth chamber. Plants were harvested 8 h, 9 days and 24 days after labelling, and separated into leaves, stems and roots. δ C values of the different parts were measured using an isotope ratio mass spectrometer, from which C excess was calculated. Water deficit decreased transpiration (P < 0.001) and increased carbon respiration (P < 0.05). Potassium application increased assimilate distribution to the roots (P < 0.05) at 9 days after labelling, more strongly for plants under water deficit. The opposite was found at 24 days (P < 0.05) with the legacy of water deficit additionally increasing assimilate distribution to roots (P < 0.05). Youngest, fully expanded leaves contained up to 47% of initial C excess at 24 days after labelling. Pulse labelling proved to be successful in shedding light on carbon allocation in relation to water and potassium availability. This technique, once adapted to field conditions, could further be used to improve fertilizer recommendations or change agronomic practices to cope with plant stress.