Agriculture, forestry and other land uses are currently the second highest source of anthropogenic greenhouse gases (GHGs) emissions. In soil, these gases derive from microbial activity, during carbon (C) and nitrogen (N) cycling. To investigate how Eucalyptus land use and growth period impact the microbial community, GHG fluxes and inorganic N levels, and if there is a link among these variables, we monitored three adjacent areas for 9 months: a recently planted Eucalyptus area, fully developed Eucalyptus forest (final of rotation) and native forest. We assessed the microbial community using 16S rRNA gene sequencing and qPCR of key genes involved in C and N cycles. No considerable differences in GHG flux were evident among the areas, but logging considerably increased inorganic N levels. Eucalyptus areas displayed richer and more diverse communities, with selection for specific groups. Land use influenced communities more extensively than the time of sampling or growth phase, although all were significant modulators. Several microbial groups and genes shifted temporally, and inorganic N levels shaped several of these changes. No correlations among microbial groups or genes and GHG were found, suggesting no link among these variables in this short-rotation Eucalyptus study.