Sediments have been considered as major sinks for microplastics, which can be ingested by benthic non-target organisms and pose long-term risks due to the likely ongoing exposure of parental and filial generations. This study aimed to investigate the particle effects of polyethylene microplastic fragments (1-45 μm) in sediment on a common freshwater benthic invertebrate, Chironomus tepperi, at four environmentally relevant concentrations (125, 250, 500 and 1,000 microplastic particles/kg sediment) using a two-generation exposure regime. Apart from traditional apical endpoints, changes to whole body metabolite and lipidomic profiles were examined using Nuclear Magnetic Resonance spectroscopy to further understand the sub-lethal effects associated with exposure to microplastics. In the parental generation, both survival and emergence showed a dose-dependent decrease with significant reductions observed at both 500 and 1,000 microplastics/kg compared to the control group, whereas growth (body length and body mass) was only affected at the highest exposure concentration. Similarly, a dose-dependent decrease in several amino acids and lipidic metabolites was observed in the parental generation, which likely reflects a physical disruption of food/nutrient acquisition, or potentially an impact on energy generation. Conversely, no significant differences were observed for growth, survival, or emergence and lactic acid was the only metabolite that differed significantly between treatments in the first filial generation which was continuously exposed to microplastics. Larvae in the unexposed first filial generation showed no differences in survival, metabolomic and lipidomic profiles which suggest that effects observed in the parental generation do not carry over to the subsequent filial generation. Overall, these results demonstrate the application of integrated apical and metabolomics/lipidomics approaches to unravel the potential organismal and physiological effects of polyethylene microplastics on a benthic invertebrate under environmentally relevant concentrations.