Forest management practices impact the amount of organic matter reaching the soil, but also the soil properties and/or vegetation composition that influence soil microbiome structure and composition. After 15 years of the last application of sewage sludge (SS) alone or in combination with CaCO3 to soils of a silvopastoral system with Pinus radiata D. Don, still some residual effects were observed in the soil chemical parameters (such as pH, exchangeable Na, Ca, or K) but bigger changes on soil bacterial families were detected. However, no significant effect of the fertilization was found in the total amount of soil organic matter or its mid-infrared spectral signature. Acidobacteriaceae, Sinobacteraceae, Bradyrhizobiaceae, Burkholderiaceae and Pseudonocardiaceae were the most abundant identified families in all treatments and light changes in their abundances were detected in the different soil treatments. However, when looking at the bacterial diversity (number of families) a strong decrease in the number of specific bacteria linked to the NF soils (Non fertilised) was observed in the SS treated soils (and this decrease was even more pronounced when SS was combined with CaCO3). Soil pH and exchangeable Al were found the main factors shaping the structure of bacterial families in the studied soils, while other factors such as total soil P, exchangeable Na, exchangeable K showed the lowest correlation with bacterial abundances. Most of correlations between soil pH and families’ abundances were negative while in the case of exchangeable Al, both negative and positive correlations were observed equally. The Thermomonosporaceae, Acidimicrobiaceae and Coriobacteriaceae families showed the highest number of significant correlations with soil chemical parameters (pH, total N, organic C, exchangeable K and Al and CEC).