Hydrocarbon contamination poses significant environmental challenges due to its persistence and adverse effects on ecosystems. Contamination of soil by petroleum hydrocarbons (PHCs) has attracted the attention of environmental scientists and engineers because of its threats to soil ecosystem services, groundwater quality, and human health. Thus, remediation of such pollutants from soil, water, etc. is extremely important. In recent years, systematic efforts have focused on developing feasible approaches for recovering PHC-polluted soils. Bioremediation through bio-stimulation (adding nutrients and electron acceptors to improve the proliferation and activity of native hydrocarbon-degrading microorganisms), as well as phytoremediation, was identified as a technically viable, profitable, and ecologically sustainable technology. Subsequently, studying microbial communities involved in soil bio-stimulation as well as phytoremediation known for its significant potential to eliminate hydrocarbons and other hazardous compounds in soil and water bodies is vital to recognize the precise microbial characteristics that regulate better-quality decontamination rates. Therefore, the field of geomicrobiology offers a promising alternative through bioremediation, utilizing microorganisms to degrade hydrocarbons. In this review, the dynamics of microbial communities (including bacteria, archaea, and fungi) intermediating the bioremediation of PHC-contaminated soils as well as water bodies through bio-stimulation in terms of activity, abundance, and taxonomic configuration will be critically analyzed, which is a geomicrobiological approach.