We assessed the pools of non-structural nitrogen compounds (NSNC) through a year, thereby addressing the question of whether mature sessile oak [Quercus petraea (Matt.) Liebl.] and beech (Fagus sylvatica L.), which differ in wood anatomy and growth patterns, exhibit contrasting seasonal dynamics of NSNC pools as previously shown for non-structural carbohydrate (NSC) pools. Seasonal fluctuations of NSNC (amino acids and soluble proteins) and NSC (starch and soluble sugars) pools were analyzed in the inner and the outer stem sapwood. In oak, NSC showed marked seasonal variation within the stem sapwood (accumulation during winter and decrease during bud burst and early wood growth), whereas in beech seasonal fluctuations in NSC were of minor amplitude. Even if the distribution and intensity of the NSNC pools differed between the two species, NSNC of the stem sapwood did not show seasonal variation. The most ignificant change in NSNC pools was the seasonal fluctuation of protein composition. In both species, two polypeptides of 13 kDa (PP13) and 26 kDa (PP26) accumulated during the coldest period in parallel with starch to sugar conversion and disappeared with the onset of spring growth. The absence of seasonal changes in total soluble protein concentration suggests that the polypeptides are involved in the internal nitrogen (N) cycling of the stem rather than in N storage and remobilization to the other growing organs of the tree.