In tropical dry forests, both the dry and the short rainy seasons have become increasingly irregular. This study replicated these conditions to investigate the effects of two water deficit cycles on Cenostigma microphyllum seedlings. Impacts were assessed by measuring growth traits, water relations, gas exchange, and dynamics of nonstructural carbohydrate (NSC) content in the whole plant under greenhouse conditions in potted plants. In the first water deficit cycle, the leaf relative water content (RWC) was maintained at the expense of a rapid drop in gas exchange. Furthermore, there was a slight accumulation of NSC, mainly soluble sugars (SS) in the stem wood and roots, to the detriment of height and stem diameter growth. In the second cycle, the leaf RWC remained 40% higher than the lowest level measured in the first water deficit, and CO2 assimilation remained twice as long in previously stressed plants. The SS content of the stems and roots was strongly correlated with the predawn leaf RWC. No strong reduction was observed in the bark stock even with the gradual increase of SS in the wood. Our data suggest that under recurrent water deficit prior to leaf drop, CO2 assimilation is maintained, with the highest possible leaf RWC, under reduced stomatal conductance. This assists in SS transport to wood and root, which is no longer used to support the growth of the aboveground parts.