Deciduous trees from dry tropical forests (DTF) exhibit high non-structural carbohydrate (NSC) dynamics across seasons. Considering that the roots are the main destination of these sugars during periods of water deficiency, the main objective of this study was to understand the role of coarse and fine roots in NSC dynamics. Cenostigma microphyllum juvenile plants grown in pots were subjected to different forms of water deficiency. Plants subjected to chronic water deficit showed greater efficiency in maintaining water status than plants subjected to water deficit alone. However, stomatal conductance was similar in both treatments. During water deficiency, the biomass of the coarse roots increased, as did the NSC concentration. After the recovery period, both variables decreased when compared with other organs, which benefited the leaf and stem biomass. Water deficiency decreases the total concentration of NSC but is more intense in plants under chronic water deficit. The root system morphology also changed under both water deficiency treatments, decreasing the specific root length and root surface area but strongly increasing the density of fine roots. More robust fine roots have a greater capacity to explore soils with low moisture. When considering changes in the climate of semi-arid regions with longer dry seasons and more irregular rainy seasons, abilities such as those of the species studied could support the survival of woody species and increase their performance.