Marine diatom Chaetoceros muelleri is characterized by lipid and carbohydrate accumulation under low nitrogen concentration without affecting biomass. To elucidate the molecular effects of nitrogen concentrations, we performed an RNA Seq analysis of C. muelleri grown under four nitrogen concentrations. Transcriptional analysis revealed that the lowest nitrogen concentrations enhanced an exacerbated transcriptional response. The observed adjustment in the expression of genes modulating protein synthesis and composition under nitrogen limitation reflects diatoms' adaptive strategies to optimize nitrogen utilization and survive in nutrient-limited conditions. They may redirect metabolic fluxes, adjust central carbon metabolism, and fine-tune energy-generating pathways to adapt to nitrogen limitation and stimulate lipid biosynthesis. These alterations can influence the physicochemical properties of the biomolecules and their potential applications in various industries.