Forest cover can be effective in reducing the changes caused by mining, especially through the recovery of organic matter stocks. The objective was to evaluate the C and N stocks in fractions of soil organic matter in bauxite-mined area under rehabilitation with forest species. The forest covers evaluated were: eucalyptus (Euc), A. peregrina (Ap) and a mixed planting of native forest species (Nat), in addition to an area without forest cover (WCov) and native forest in an unmined area (NV). The fertilization treatments studied were a standard adopted by the company (SF), organic fertilizer (OF), chemical fertilizer (CF) and OF + CF. The total stocks of C and N from particulate organic matter (POM), mineral-associated organic matter (MOM), microbial biomass (MB) and labile C (LC) were estimated, as well as the C/N ratio and the carbon management index (CMI). The influence of the presence or absence of litter was evaluated, as well as the roots on C and N stocks in the soil. The stocks of total and labile C, CMI and MBC did not differ between the forest covers studied in the 0-60 cm layer, being lower than those in NV and higher than those found in WCov. The other variables (TN, CMOM, NMOM, CPOM, NPOM and MBN) were higher only in the NV. Mining causes reduction of organic matter fractions; however, forest cover increase the stocks of TOC, LC and CMI. Roots are more associated with the recovery of C and N stocks than litter and trunk biomass.