Allocation of nitrogen (N) and phosphorus (P) among plant organs is an important factor regulating growth rate, which is a key ecological process associated with plant life-history strategies. However, few studies have explored how N and P investment in photosynthetic (leaves) and non-photosynthetic (stems and roots) organs changes in relation to depletion of each element. We investigated nutrient concentrations of plant organs in relation to whole-plant nutrient concentration (total nutrient weight per total biomass) as an index of nutrient status of each individual using the saplings of the 13 species in three tropical rain forests with contrasting N and P availabilities (tropical evergreen forests and tropical heath forests). We found a steeper decrease in foliar N concentration than foliar P concentration with decreasing whole-plant nutrient concentration. Moreover, the steeper decrease in foliar N concentration was associated with relatively stable N concentration in stems, and vice versa for P. We suggest that the depletion of N is associated with a rapid dilution of foliar N because the cell walls in non-photosynthetic organs function as an N sink. On the other hand, these species can maintain foliar P concentration by decreasing stem P concentrations despites the depletion of P. Our results emphasize the significance of non-photosynthetic organs as an N sink for understanding the variation of foliar nutrient concentrations for the tree species in the three Bornean rain forests with different N and P availabilities.