Mixed plantations of Eucalyptus and N-2-fixing trees are ecologically beneficial because they stimulate organic matter cycling and increase carbon (C) and nitrogen (N) pools in the soil. However, the microbial mechanisms that contribute to the improvement of C and N dynamics remain poorly understood in managed forest ecosystems. Here, we evaluated interactions between the bacterial community and biological functions involved in C and N cycles in the soil and litter layers resulting from pure or mixed Eucalyptus grandis and Acacia mangium plantations. We hypothesized that the mixed plantations induce changes in the bacterial community that would drive increases in C and N pools in soil and litter layers. We established a field experiment with treatments including pure E. grandis without (E) and with nitrogen fertilization (E + N), pure A. mangium (A), and mixed E. grandis and A. mangium (E + A). Soil and litter from all treatments were sampled 27 and 39 months after planting. We evaluated the soil and litter bacterial community and biological functions involved in C and N cycles (i.e., microbial and enzyme activities, functional gene abundance, and soil-litter nutrient cycling). The treatments A and E + A showed an increase in C and N contents in the organic soil fractions. We found higher bacterial diversity and OTU richness in soil and litter, and higher nifH gene abundance in the soil under A and E + A, when compared to pure E. grandis (especially E + N) plantation. Our data suggest that the total N content influences the bacterial community structure of the litter, which undergoes alterations according to the treatment and forest age. Equally, Rhizobium, Bradyrhizobium and Sphingomonas showed a positive correlation with nifH and soil N. Our study provided evidence that changes in the microbial community in mixed A. mangium and E. grandis plantations is correlated with increased C and N cycling. These findings have implications for increased productivity and environmental sustainability, besides allowing for the optimization of mineral fertilization in forest plantations.