Coupling chemical oxidation with bioremediation could be a cost-effective system to cope with soil and groundwater pollution. However, the effects of chemical oxidation on autochthonous microbial communities are scarcely known. A detailed analysis that considers both the efficiency of the two technologies and the response of the microbial communities was performed on a linear alkylbenzene-polluted soil and groundwater samples. The impacts of a modified Fenton’s reaction (MFR) at various dosages and of permanganate on the microbiota over 4 weeks were assessed. The permanganate and MFR negatively affected microbial abundance and activity. However, the resilience of certain microbial populations was observed, with a final increase in potential hydrocarbon-degrading populations as determined by both the alkB gene abundance and the predominance of well-known hydrocarbon-degrading phylotypes such as Rhodococcus, Ochrobactrum, Acinetobacter and Cupriavidus genera as determined by 16S rRNA-based DGGE fingerprinting. The assessment of the chemical oxidant impact on autochthonous microbiota should be considered for the optimization of coupled field remediation technologies.