As a result of climate and energetic crises, as well as the environmental implications of fossil fuel consumption, the use of biofuels has expanded in recent decades. In Brazil, biodiesel is used in blends with diesel (also known as B12) and ethanol in blends with gasoline (also known as E27). The growing use of such blends increases the risk of biofuel contamination in soil, surface, and groundwater. In addition to the identification and quantification of the pollutants to assess the effectiveness of the bioremediation treatments in biofuel/fossil fuel blend impacted soils, elucidating changes in the specific functional profiles related to hydrocarbon degradation brings also important information about the direct impact of these approaches about the responses of the main actors of the bioremediation, the microorganisms. Such knowledge is scarce and may be of pivotal relevance to design customized bioremediation protocols, contributing to optimize and accelerate the pollutant removal and recovery of impacted areas. This study aimed to extensively describe the dynamics of hydrocarbon degradation functional profiles of four areas deliberated polluted with E10, E25 or B20 and subjected to different bioremediation treatments (i.e., injection of anaerobic electron acceptors, biosparging, or bioaugmentation). Metagenomic shotgun sequencing results indicated that long-term polluted areas that have never been submitted to any bioremediation treatment had a specific functional profile different from the treated areas. Interestingly, the same hydrocarbon degradation genes were enriched in all areas regardless the type of bioremediation applied. However, the taxa associated with these genes were different between the areas under different blend contamination and/or bioremediation treatment, demonstrating the importance of the functional redundancy to maintain the soil ecosystem functioning. the keystone species in the same areas, we confirmed in the current work that Finally, several of the keystone species in the community are hydrocarbon degraders, showing that these taxa can be targets for biostimulation in future soil remediation processes. Altogether, these findings contribute to the understanding of the effects of bioremediation treatments over the functional genetic potential of the microbiome in biofuel/petrofuel impacted soils, helping to define the most appropriate technique according to the type of contamination.