Forest residues are frequently used as energy sources by Brazilian forest companies. The removal of such residues is known to reduce wood productivity, especially when fertilizer application rate is low. This study aimed to evaluate after two forest rotations the effects of forest residue management on wood productivity when fertilizer is applied at a high rate; and the effect of timber harvest intensity on soil organic matter and microbial activity. We assessed tree growth, soil microbial biomass and activity, and we fractionated soil organic matter (SOM) via its oxidation resistance. These assessments were performed after conducting a field trial comparing harvest residue management over two successive rotations in the same plots. We found no significant effect of treatments on wood productivity when the residues were removed for the first time; however, wood productivity reduced by 15% during the second rotation with residue removal even with high rates of fertilizer application. Further, 40% reduction in microbial biomass and soil respiration was noted with forest residue removal. At the reestablishment time, the SOM in the top soil (0–0.05 m layer) was 25% lower at the site where the forest residues were removed, and this difference increased to 50% at 300 days after the reestablishment. This reduction was found mainly in the SOM labile fraction.