In terrestrial environments, soil organic matter (SOM) is the largest organic carbon (C) pool. The quantity and quality of organic carbon in soils can be affected by vegetation through influencing the inputs and outputs of SOM. We examined how storage and quality of C in SOM were affected by vegetation under grass cover or single and a polyculture plot of Betula pendula, Alnus glutinosa and Fagus sylvatica. An acid hydrolysis approach was used to quantify three SOM fractions differing in biodegradability. Tree species identity and stand composition had no significant effect on the total amount of C stored in different SOM fractions to a depth of one meter. However, when examining individual SOM fractions in the upper layers of the soil profile, significantly more C was stored in the putatively more labile fractions 1 and 2 under F. sylvatica and A. glutinosa, respectively. In deeper soil layers, the highest storage of recalcitrant organic C was found under the tree polyculture. The vertical distribution of these three soil organic C pools was compared to C inputs via decomposed leaf litter. Our data indicated that in the tree species polyculture, combining litter inputs of multiple species can have a positive impact on the accumulation of acid resistant recalcitrant C in deep soil layers in 4 years. This C fraction has the greatest potential for long-term sequestration.