Microplastic (MP) toxicity has recently been explored in various marine species. Along with the toxicity of plastics polymer itself, additional substances or pollutants that are absorbed onto it may also be harmful. In the present study, we investigated the combined impacts of polyethylene microplastics (PE MPs) and an organic pollutant (Benzo(a)anthracene, BaA) on Manila clam Ruditapes philippinarum during a one-week exposure. Two PE MPs concentrations (26 μg L−1 and 260 μg L−1) and one BaA concentration (3 μg L−1) were tested. The clams were exposed to BaA and PE MPs either alone or in combination. BaA and PE MPs were incubated before the combined exposure. The biological effects of PE MPs and BaA on the clams were evaluated by considering several assays such as feeding rate, anti-oxidant enzyme activities, and the expression levels of stress-related genes. The feeding rate significantly decreased in individual PE MPs and individual BaA groups while it remained unchanged in combined groups. Superoxide dismutase (SOD) was the most affected among the biochemical parameters. Malondialdehyde (MDA), and glutathione peroxidase (GPx) activities were slightly affected, whereas no changes were observed in glutathione s-transferase (GST) activities. CYP1A1, CYP3A4, and HSP70 gene expressions displayed slightly significant changes. Considering all stressor groups, high PE MPs exposure (260 μg L−1 PE MPs) more effectively altered the biological parameters in the clams compared to individual low PE MPs and BaA exposure, and their combination. The results also indicated the negligible vector role of PE MPs to transport BaA into the clam tissues. Display omitted •The feeding rate of clams substantially declined by polyethylene MP and Benzo(a)anthracene exposure.•The exposure of polyethylene MP and BaA influenced SOD, MDA and GPx activities bot not GST.•The regulation of genes HSP70, CYP1A1 and CYP3A4 were affected by polyethylene MP and BaA exposure.•BaA efficiently accumulated in clam tissues.•Polyethylene MP has a negligible vector role in transporting BaA to clams.