Bacillus cereus bacteria and their by-products were used as surface-active agents for surface hydrophobicity of the apatite in the flotation process leading to phosphate ores' enrichment. Recently, proteomics is used to investigate the biochemical processes through discovering new proteins or investigating protein-protein interactions. In this work, we investigated the physicochemical behavior of pure apatite and quartz minerals in the presence of Bacillus cereus using zeta-potential, FTIR, and hydrophobicity measurements. Our results indicated that isoelectric point (IEP) occurred at pH 4.7 for apatite and 2.1 for quartz mineral. Bacillus cereus treatment decreased IEP of apatite to 1.8; while there was no significant change in IEP value of quartz. We used comprehensive proteomic profile analysis of Bacillus cereus in the presence of apatite mineral to identify the biological mechanism and molecules involved in such enrichment capacity. Our data identified the up-regulated Surface Layer (S-Layer) protein in this bacterial strain to be associated with the best mineral yield.