The natural ecology and human health have been adversely affected by environmental pollution resulting from organic pollutants, heavy metals, and potentially hazardous waste products. While soil naturally contains heavy metals, rapid industrialization and human activities like uncontrolled use of agrochemicals have significantly increased their concentrations globally. Bioremediation provides an environmentally acceptable and effective approach to recovering areas damaged with toxic compounds by utilizing the intrinsic biological techniques of microbes and plants to eliminate unstable chemicals. Recent research is enhancing the ability of naturally occurring microbes to cleave detrimental compounds that are released in the ecosystem. Among distinct bioremediation methods, microbe-based technique stands out for their effectiveness, lack of toxic end-products, and the natural presence of microbes that can biodegrade nutrients from surface contaminants. These microbes facilitate both in situ and ex situ bioremediation processes effectively. The advancement of bioremediation technology depends on comprehending the complexities of biodegradation mechanisms. The toxic petroleum hydrocarbons and their associated by-products are effectively removed economically and effectively by using an integrated approach that combines biostimulation and bioaugmentation. Thus, the current chapter will elaborate on the microbe-based remediation of the hydrocarbons along with its limitations and prospects.