The impact of Erythrina poeppigiana on soil characteristics, at three different positions relative to the shade tree and from three different soil depths, was evaluated in pairs of comparable Costa Rican coffee farms (organic and conventional) in 2000 and 2004. In the conventional system at 0-5 cm, higher C and N concentrations were found close to the shade tree versus the positions 2 m from the trunk (5.04 vs. 4.18%). This positive effect could influence only 20% of the farm area when high population of E. poeppigiana were used. This finding highlighted the importance of E. poeppigiana in maintaining SOM levels. In contrast, the organic system showed similar C and N concentrations for all positions probably due to an even distribution of pruning residues and to the use of organic amendments. A trend to higher total C and N concentrations for organic farms in comparison to conventional farms was found. No significant temporal changes in soil C or N concentrations were found between 2000 and 2004.