Nowadays, nanoplastics (NPs) are one of the main concerns regarding plastic pollution. The increasing presence of plastic particles, fibers and fragments in the marine environment pose an additional risk to both, wild and cultured fish. Ingestion is the main mechanism by which particles are internalized. Thus, this study evaluated the impact of a diet containing NPs in one of the most cultivated species across the Mediterranean Sea, the European sea bass (Dicentrarchus labrax). Polystyrene NPs (50 nm) were supplied in the food for a period of 21 days and the transcriptomic changes were measured in the intestine through RNA-seq. Additionally, enzymatic and bactericidal activities were measured in the liver or serum, respectively of the same fish to evaluate the organism stress. No significant changes in the enzymatic activities were observed in the liver, whilst the seric bactericidal activity decreased by NPs dietary treatments. This suggests that ingestion of NPs at low dosages might have an impact on fish health. In addition, our data suggested that NPs impact some important biological pathways related to fish morphogenesis, organ development, membrane receptors, and fish immunity. These routes are extremely important for fish development and growth and can have long-term impact, since the early stages of fish are the most sensitive to this kind of pollution. This study provides information on the impact of the ingestion of NPs in sea bass and can serve as a basis for future investigations on the prevention and treatment of such pollutants in aquaculture.