Slash-and-burning forest clearing is a common practice in the Amazon region. In order to understand to what extent this may change the basic mechanisms of soil fertility, we analyzed the structure of the microbial community in forest and deforested soils and relate these to changes in soil chemical factors. Deforestation decreased soil organic matter (OM) content and factors linked to soil acidity, and raised soil pH, base saturation, and the concentration of exchangeable bases. Concomitantly to expected changes in soil chemical factors, we observed an increase in the alpha diversity of the bacterial microbiota and relative abundance of putative copiotrophic microbes such as Actinobacteria, and a decrease in the relative abundance of bacteria such as Chlamydiae, Planctomycetes and Verrucomicrobia in the deforested soils. We did not observe an increase in genes related to microbial nutrient metabolism in deforested soils; however we did observe changes in community functions, which included increases in DNA repair, protein processing, modification, degradation and folding functions. In addition there were changes in composition of the bacterial groups associated with metabolism-related functions. Co-occurrence microbial network structures identified distinct phylogenetic pattern for forest and deforested soils and opened the possibilities to investigate relationships between Planctomycetes and Al content, and Actinobacteria and nitrogen sources in Amazon soils. The results support taxonomical and functional adaptations in the soil bacterial community following deforestation. We hypothesize that these microbial adaptations may serve as a buffer to drastic changes in soil fertility after slash-and-burning deforestation in the Amazon region.