Gold mining has been a practice in Egypt for thousands of years. Egypt has numerous ancient gold mine sites and abandoned tailings that still exist to date. These sites contain waste materials that continue to pose environmental risks due to the presence of toxic heavy metals. The aim of this chapter was to explore the role of microorganisms in the rehabilitation of these ancient gold mines. Microbes are known to help in the bioremediation of the toxic elements present in gold mines using several mechanisms such as biosorption, bioaccumulation, bioprecipitation, and bioreduction, which play significant roles in the immobilization or concentration of metals. They also have a role in the recovery of gold from low-grade ores using bioleaching, biooxidation, or biocyanidation to solubilize the targeted metal making it more accessible for further processing or recovery. Microbial-assisted phytoremediation of gold mine sites is also possible due to the ability of these microorganisms to produce plant growth hormones that help these plants to survive in these difficult and often toxic environments. In this chapter we identify these microbes and discuss their potential roles in the rehabilitation of ancient gold mines in Egypt. The chapter is concluded by summarizing the main points discussed and providing some future directions to fulfill the existing gap in this research area in Egypt.