The aim of this research was to study the impact of nitrogen starvation on the production of two major secondary metabolites, fatty acids and carbohydrates, in two microalgae: Nannochloropsis sp. and Haematococcus pluvialis. The major response to nitrogen starvation in both algae occurred within the first 2 days, accompanied by a sharp reduction in chlorophyll content. However, the pattern of the response differed between the two microalgae. In H. pluvialis, the first response to nitrogen starvation was intensive production of carbohydrates, accumulating to up to 63% of dry weight by day 1; on day 2, the total carbohydrate content decreased and was partially degraded, possibly to support fatty acid synthesis. Under these conditions, H. pluvialis accumulated up to 35% total fatty acids in the biomass. In Nannochloropsis sp., the immediate and major response, which was maintained throughout the entire period of exposure to stress, was production of fatty acids, accumulating up to 50% of dry weight, while carbohydrate content in the biomass remained stable at 18%. In addition, we tested the effect of the lipid-synthesis inhibitor sesamol, known to inhibit malic enzyme, on the balance between total fatty acid and carbohydrate contents in H. pluvialis and Nannochloropsis sp. In both cultures, sesamol inhibited fatty acid accumulation, but the carbohydrate content was reduced as well, albeit to a lesser extent. These findings demonstrate the complexity of the stress-response and the potential link between fatty acid and carbohydrate synthesis.