Graphical abstract Highlights • Decreasing the cell viability by strong interaction and ROS generation. • Nano-SIMS could prove the contribution of hematite to intracellular iron, directly. • Restricting the BaP bioaccessibility to the bacterium. Abstract Iron oxides are reactive inorganic soil components that play an important role in the fate and transport of organic pollutants. Here, hematite was selected to investigate its effect on the biodegradation of benzo[a]pyrene (BaP) by Paracoccus sp. strain HPD-2. Approximately 60% of the total BaP was degraded in the absence of hematite after 7 days but only 30.8 and 20.8% of that was degraded after the addition of 10 and 20 mg mL–1 hematite, respectively, indicating that the addition of hematite could significantly inhibit the biodegradation of BaP (P < 0.05). The hematite also lowered bacterium activity by coating the cells and by generating reactive oxygen species that destroyed the cells. Two-photon confocal laser scanning microscope images showed that the addition of hematite substantially decreased the amount of BaP combined with the bacterium, and this also enabled us to observe directly the migration and regression of BaP in the interaction between HPD-2 and hematite. Higher death ratio of HPD-2 might lower the BaP access to live cells because dead cells have a higher adsorption affinity for BaP than live cells. These observations enhance our understanding of the mechanisms by which metal oxides, organic pollutants and degrading-bacteria interact during the biodegradation process. [ABSTRACT FROM AUTHOR]