Soil microorganisms are a vital component and regulate a myriad of functions of forest ecosystems. Anthropogenic disturbances in natural forests could drive major shifts in plant and microbial communities resulting in substantial biogeochemical alterations. We evaluated the effect of anthropogenic disturbances in soils in an Andean temperate forest with different levels of degradation: i) mature forest (MF), ii) secondary forest (SF), iii) degraded forest (DF), and iv) deforested site converted into a prairie (DP). We quantified total carbon, nitrogen, and phosphorous (TC, TN, and TP) soil and nutrient available pools. Microbial communities’ structure and diversity were assessed under each condition via NGS-Illumina sequencing and microbiome analysis. There were no significant differences in TC, TN, and TP across the forested states (MF, SF, DF). The deforested site condition presented significantly higher surface soil TC, TN, and TP and the lowest C:N, C:P, and N:P ratios. The bacterial microbiome was dominated by Proteobacteria (45.35±0.89%), Acidobacteria (20.73±1.48%), Actinobacteria (12.59±0.34%), and Bacteroidetes (7.32±0.36%) phyla in all sites. Yet, there were significant differences at the genus level across conditions. The soil fungal community was dominated by the phyla Ascomycota (42.11±0.95%), Mortierellomycota (28.74±2.25%), Basidiomycota (24.61±0.52), and Mucoromycota (2.06±0.43%). The DP soil microbiome was significantly less diverse in bacteria (D' = 0.47±0.04); however, it was significantly more diverse in fungi (H' = 5.11±0.33). Forest to prairie conversion facilitated the introduction of novel bacterial and fungal groups associated with livestock grazing. The AOB community rose as a dominant group in the DP soils along with a reduction in the ECM fungi community. The surface soil microbiome was surprisingly resistant to forest degradation and did not show a clear progression along the degradation gradient. However, the microbiome was strongly altered after forest conversion into grassland.