Cyanobacteria are the main autotrophs and N2‐fixing (diazotrophic) organisms in large parts of the oligotrophic global ocean, where generally all heterotrophic production depends on their activity. Amino acids (AAs) from cyanobacteria are essential macronutrients for these heterotrophic food webs, yet little is known about the de novo synthesis of AAs during N2 fixation. Through a combination of bulk and amino acid nitrogen (AAN) specific analyses of field based N2 fixation experiments, we demonstrate that the de novo synthesis of 13 AAs accounted for the majority of bulk N2 fixation rates at four stations in the central Baltic Sea in July 2015. Slow AA turnover times of 87 ± 14 d coincided with low phosphate concentrations and high cell‐carbon biomasses of unicellular cyanobacteria. Very fast turnover times of 17 ± 3 d coincided with high phosphate concentrations and undecayed Nodularia spumigena cells, but unexpectedly also with phosphate depletion and decayed N. spumigena cells. In a decayed bloom, volumetric N2 fixation rates into AAN provided a much better estimate of the net incorporation of N2 into biomass than fixation into bulk nitrogen that rather reflected gross N2 fixation. In an undecayed bloom, the turnover times of 13 AAs can be predicted from a single bulk N2 fixation rate. This is the first direct evidence that the very late, decayed stage of a cyanobacteria bloom can be a flashpoint of very fast AA turnover during N2 fixation with hitherto uncharacterized consequences for heterotrophic food webs and diazotroph N inputs to the global ocean.