Agroforestry is indicated as a farming practice suited to enhance ecosystem services generated by cropping systems. However, farmers are often reluctant to implement agroforestry systems due to the potential yield loss of crops. In a field trial, soybean was intercropped with poplar short-rotation-coppice rows in an alley-cropping system with 13.5 m wide alleys, in order to assess the effect of tree presence on soybean yield and quality. The light availability (LA) was significantly affected by the tree presence, with an increasing effect along the season due to tree growth, being at its lowest in the tree–crop interface positions (West and East). Significant effects of the tree-distance and LA were registered on soybean yield, with the highest reduction of soybean yield in the West (−78%) and East (−35%) positions. Crude fat content in soybean grain did not vary among positions in the alley, while crude protein content was the lowest in the most shaded position (West −8% than the highest value). The assessment of spatial variability among plots of measured soil characteristics highlighted no significant effect of pedological conditions upon soybean yield. Thus, in our study, the LA effect was more important than soil characteristics in determining a detrimental effect of competition for resources between soybean and poplar. Conversely, soybean quality was affected by soil characteristics, since crude fat significantly correlated with soil nutrients, pH, soil organic matter and soil texture.