Coastal seas like the North Sea have been subject to major changes in nutrient inputs over the last decades, resulting in shifts of limiting nutrients for phytoplankton communities. Here, we investigated the seasonal and spatial distribution and synthesis patterns of individual amino acids and distinct fatty acid groups and show how these were affected by different nutrient limitations in natural coastal phytoplankton communities. Nitrogen limited communities exhibited substantially slower synthesis of essential amino acids compared to synthesis of nonessential amino acids. In short-term nutrient addition experiments, this trend was reversed immediately after N addition to levels found under not limiting conditions. On the contrary, phosphorus limited communities showed no such shift in amino acids. Both N and P limitation induced a shift from structural to storage fatty acids with a concurrent decrease in the synthesis of poly-unsaturated fatty acids. Reversed effects in fatty acid synthesis after N or P addition were only apparent after 72 h, when they could be found in both fatty acid biosynthesis and concentrations. The different strategies of qualitative and quantitative regulation of different biomolecule synthesis under nutrient scarcity may have far-reaching consequences for the phytoplankton's nutritional value. Higher trophic levels may have to cope with the loss of essential amino acids and poly-unsaturated fatty acids in nutrient limited phytoplankton, which could induce changes in the structure of food webs.