Phosphate ores are considered as high-value geo-resources. Microbial resources from this environment play a crucial role in the biogeochemical cycle of phosphorus. However, they are still under-characterized, especially in the context of water pollution control and wastewater treatment. The main objective of this study was to investigate the microbial diversity of a soil sample collected from a Tunisian phosphate mine and its phosphorus removal capability. Soil DNA was extracted and high-throughput 16S rRNA gene amplicon sequencing was carried out using Illumina Miseq Platform. Batch tests were performed to characterize the phosphorus adsorption efficiency of this sampled soil. Results revealed a predominance of Actinobacteria. Analysis at the genus level showed the presence of several bacterial taxa evolving in multiple phosphorus transformations, such as phosphorus solubilization or immobilization through various physiological processes. Characterization of bioavailable soil elements showed a high mineral salt content. Characterization of phosphorus adsorption from aqueous solution with high mineral contents by the raw soil sample showed a chemisorption type fitting the pseudo-second-order model with a removal capacity of around 12.75 mg P g−1 of raw soil. In addition, putative microbial stains evolving in intracellular phosphorus accumulation were isolated from this sample. These results yielded new insights into microbial diversity within the phosphates mining area. Moreover, raw soil as well as indigenous bacteria could be of potential use in various biotechnological applications related to soil fertilization and phosphorus pollution control in water and wastewater treatment.