Recently, wastewater treatment plants (WWTPs) have been stressed by increased levels of hydrocarbons (e.g., BTEX) generated by the industry. Due to their toxic effects and high persistence in water matrices, hydrocarbons can hinder WWTP performance. These pollutants also pose significant health risks, including damage to the human immune system, central nervous system, liver, kidney, and potential carcinogenic effects. Consequently, the proper treatment of the hydrocarbon-containing wastewater becomes imperative. Biodegradation by natural populations of microorganisms represents one of the primary mechanisms by which hydrocarbons can be properly eliminated from wastewater. It is widely considered one of the most cost-effective, environmentally friendly, and practical ways of dealing with these pollutants. However, a relatively high concentration of hydrocarbons in wastewater may inhibit microbial activity due to a toxic shock to microorganisms. To address this issue, the pre-treatment of wastewater by advanced oxidation processes (AOPs) is promising. The fenton process, one of the most used AOPs, can effectively treat wastewater containing high organic contents in complex matrixes. Furthermore, the presence of Fe2+ and Fe3+ ions in this process can have a coagulation and oxidation function, boosting the treatment performance. Thus, in this study, batch reactors under nitrifying aerobic and denitrifying anoxic conditions are operated to evaluate and compare the biodegradation of raw and fenton-pretreated wastewater (FWW). Moreover, we investigate the interaction effects of the precipitates generated from the fenton process and hydrocarbon concentration on the overall treatment efficiency. The outcomes of this study are expected to provide new perspectives on the optimization of fenton-integrated biological processes for satisfactory performance in the presence of hydrocarbons.