Phenotypic plasticity enables plants to adjust their morphology and phenology to variable environments. Although potentially important for crop breeding and management, the physiology and genetics of plasticity traits are poorly understood, and few models exist for their study. In the previous paper of this series, the structural–functional model EcoMeristem was described and field validated for vegetative-stage rice. This study applies the model to an experimental study on phosphorus deficiency effects on two morphologically contrasting rice cultivars, IR64 and Azucena, grown in controlled environments under hydroponics culture. Phosphorus deficiency caused severe biomass growth reductions in the shoot but not in the root, thus increasing the root / shoot weight ratio. It also inhibited tiller formation and leaf elongation, prolonged the phyllochron, and increased carbohydrate reserve pools in the plant. Analysis aided by the model identified inhibition of leaf extension and tillering as primary effects of the stress. Physiological feedback probably led to longer phyllochron, greater reserve accumulation and root growth stimulation. The main effect of P deficiency appeared to be a reduction in demand for assimilates in the shoot while photosynthetic radiation use efficiency remained nearly constant, resulting in spill-over of excess assimilates into reserve compartments and root growth. The results are discussed in the light of future applications of EcoMeristem for phenotyping and genetic analyses of phenotypic plasticity.