The use of imidacloprid (IMI) and its formulated products in agriculture is a risk to aquatic organisms due to deposition into waterways from runoff and aerial spraying. However, there is limited information on the potential effects of this pesticide on commercially important shellfish, such as oysters. We investigated the impacts of IMI and Spectrum 200SC (IMI formulation) on the activity of the enzymes Glutathione-S-transferase (GST), Catalase (CAT) and Acetylcholinesterase (AChE), in different oyster tissues including the gill, adductor muscle and digestive gland. We also investigated the condition index and fatty acid composition of the flesh of oysters after 2 weeks exposure. The concentrations of IMI in the different tissues was assessed using Liquid Chromatography-Mass Spectrometry (LC-MS) after QuEChERS extraction. Higher concentrations of IMI residues were detected in the adductor muscle of the oysters, followed by the gills and with the lowest amounts recovered from the digestive gland across all the concentrations tested. IMI and Spectrum 200SC significantly affected the gill AChE activity at 2 mg/L, but digestive gland CAT, and gill and digestive gland GST were impacted at environmentally relevant concentrations (0.01 and 0.05 mg/L). In the whole oyster, 2 weeks exposure to IMI (≥0.01 mg/L) resulted in a proportional increase in saturated fatty acids (SFA), altered the polyunsaturated fatty acid (PUFA) to SFA ratio and altered the omega 3 fatty acids (n-3) to omega 6 fatty acids (n-6) ratio, but there were no effects on the condition index of the oyster. Although the oysters responded differently to the formulated product, there was no consistent difference in the sublethal effects of analytical IMI and Spectrum 200SC. This study showed that exposure to IMI and Spectrum 200SC can significantly affect the biochemical processes and metabolites in oysters, with implications for food quality and safety.