Soil contamination by heavy metals through the application of a phosphate fertilizer is a key issue for sustainable agriculture. Among contaminants, cadmium (Cd) is considered the most hazardous to human beings’ health and the surrounding environment. X-ray diffraction (XRD), combined with binocular mineralogical analysis and chemical analysis, was used to determine the C(I) and C(II) layers’ composition. In the C(II) (+71 µm)-size fraction, the presence of carbonate-fluorapatite, illite, and montmorillonite was revealed, whereas in the C(I) (−71 µm)-size fraction, carbonate-fluorapatite, calcite, quartz, sanidine, clinoptilolite, and taramovite were identified. The P2O5 and CaO contents were greater in the C(II) layer than that in the C(I) layer, whereas SiO2, MgO, CO2, Cd, Zn, and COrg were higher in the C(I) layer than that in the C(II) layer. The bioleaching of Cd from phosphate rock samples from the Kef Eddour deposit was investigated using three bacterial strains isolated from the local phosphate environment. A decrease in cell viability was noticed when the phosphate C(I) and C(II) samples showed toxicity in the samples. In addition, the isolated bacteria, which were initially moderately hydrophobic, changed to strongly hydrophobic. The use of the consortium (S1 + S2 + S3) was the most powerful combination to reduce the Cd content, which increased from 13.31% to 29.07% using S3 and the consortium (S1 + S2 + S3), respectively, when the C(II) (+71 µm)-size fraction sample was added to the medium. The same result was shown when the C(I) (−71 µm)-size fraction sample was used. The isolated strains could be used as a biological tool for bioleaching.