Persistent organic pollutants, such as polychlorinated biphenyls (PCBs) and polybrominated diphenyl ethers (PBDEs), existing as mixtures in the environment, pose significant risks to ecosystems and human health. Removing these pollutants from contaminated environments, i.e. remediation, offers a solution to this global issue. This study investigated the effectiveness of bioremediation strategies, specifically bioaugmentation (BA) and biostimulation (BS), in sediment microcosms using historically contaminated sediments from shipbreaking yards in the heavily industrialized area of Aliağa, İzmir. Microbial analyses revealed 37.6% abundance of Chloroflexi-related microorganisms in the sediments, which were subsequently enriched for BA treatment. BS treatment involved adding micronutrients to stimulate native microbial activity. BA and BS achieved higher removal efficiencies for total PCBs (14% and 19%, respectively) and PBDEs (33% and 24%) compared to natural attenuation (12% for PCBs and 8% for PBDEs) set, proving the importance of external amendments for better removal. Degradation rates for PCBs were higher in BA (0.00124 chlorine per biphenyl per day-Cl/bp/day) than in BS (0.00085 Cl/bp/day) whereas PBDE degradation was faster in BS (0.00945 bromine per diphenyl ether per day-Br/dp/day) compared to BA (0.00741 Br/dp/day). Although BA and BS strategies reduced total PCB and PBDE concentrations, the formation of lower halogenated congeners indicated an ecotoxicological risk. PCB-52 exhibited consistently high risks while BDE-28 escalated to high risk in BS, and BDE-153 fluctuated between high and moderate risks across all treatments. These findings emphasized the importance and necessity of conducting laboratory-scale studies prior to in situ bioremediation applications to evaluate removal efficiencies and potential risks.