Phosphorus (P) -rich soils developed in phospharite areas while P-deficient soils are ubiquitous in subtropical areas. Across such the contrasting nutrient environments, it is little known how metabolites are involved for archiving optimal storage of energy and nutrients in plant seeds. Here we measured metabolites, element concentrations and stoichiometric ratios of Quercus variabilis acorns at the early (July), middle (August) and late (September) stages at geological-derived P-rich and P-deficient sites in subtropical China. Our results showed that the acorns of oak populations between two site types were significantly discriminated, at three stages, by metabolites (predominantly sugars and organic acids) and by ionome (majorly protein/nucleic acid (N, P, S) and enzyme (Mn and Cu) -related elements). These biomarkers were mainly linked to the carbon and nitrogen metabolisms, especially, pentose phosphoric acid pathway, in acorns. Moreover, these discriminating metabolites were correlated with N, P, S, Mg and Mn in acorns while they both were associated to certain extent with N, Mg and Mn in soils across two site types. These results suggest that for developing seeds, carbon and nitrogen metabolism could be a key mechanism for in situ plants to copy with variable nutrients in soils.