Phenotypic plasticity can mask population genetic differentiation, reducing the predictability of trait-environment relationships. In short-lived plants, reproductive traits may be more genetically determined due to their direct impact on fitness, whereas vegetative traits may show higher plasticity to buffer short-term perturbations. Combining a multi-treatment greenhouse experiment with global field observations for the short-lived Plantago lanceolata, we 1) disentangled the genetic and plastic responses of functional traits to a set of environmental drivers and 2) assessed the utility of trait-environment relationshisps inferred from observational data for predicting genetic differentiation. Reproductive traits showed distinct genetic differentiation that was highly predictable from observational data, but only when correcting traits for differences in their (labile) biomass component. Vegetative traits showed higher plasticity and contrasting genetic and plastic responses, leading to unpredictable trait patterns. Our study suggests that genetic differentiation may be inferred from observational data only for the traits most closely related with fitness.