Forest harvesting operations may have a significant impact on soil physical properties by reducing its porosity and organic functions. Soil variations, in particular bulk density and total porosity, caused by external perturbations as soil becomes compacted due to machinery passes, can lead to changes in biogeochemical cycles that have consequences on soil ecosystems. This study investigated how the impact of forest operations and the elapsed time from harvest can influence: (1) the physical-chemical characteristics of soil and (2) the nitrogen-fixing and nitrifying microbial communities. The study area is located inside the Regional Park of Migliarino, San Rossore, Massaciuccoli (Pisa, Italy). In the study area, the soil has been classified as recent sands with sandy loam texture and slightly calcareous (USDA Soil Taxonomy classification). Soil samples were collected in patchy cut areas (strip cut) of Pinus pinea stand that was harvested in two steps: half area in 2006 and the rest in 2011. Soil samples were collected also in a control area (not harvested) with similar stand and soil characteristics. Statistical analysis was preceded by a test of normality (Kolmogorov-Smirnov test) and a variance homogeneity test (Levene's test). Considering the dependence of the variables studied (physical and chemical soil characteristics), a MANOVA test and a post hoc Tukey HSD test were applied to determine statistical difference among the three treatments: harvested 2006, harvested 2011 and not harvested. The results did not indicate significant variations to the parameters of shear and penetration resistance, though soil bulk density and total porosity were significantly altered in the short period since forestry operations occurred. These physical changes induced qualitative (presence/absence and number of species) and quantitative (abundance and spatial evenness of the species) variations in the nitrogen-fixing and nitrifying microbial communities.