Spirulina is consumed worldwide, in the form of food or dietary supplements, for its nutritional value and health potential. However, these products may contain cyanotoxins, including hepatotoxic microcystins (MCs), produced by cyanobacterial contaminants. The French spirulina market has the particularity of being supplied half-locally by approximately 180 small-scale spirulina production farms. Data about this particular production and possible contaminations with other cyanobacteria and MCs are scarce. Thus, we collected the results of MC analyses and total cyanobacteria counts, carried out between 2013 and 2021, from 95 French spirulina producers who agreed to share their data. These data consisted of MC concentrations determined with an enzyme-linked immunosorbent assay (ELISA) using 623 dry spirulina samples and 105 samples of spirulina cultures. In addition, potentially unsafe samples of dry spirulina were further investigated through mass spectrometry, as duplicate analysis. We confirmed that the situation of the French spirulina production stayed within the safe regulatory level in terms of MC levels. On the other hand, the inventory of cyanobacterial contaminants, based on 539 count results, included 14 taxa. We present their prevalence, interannual evolution and geographical distribution. We also suggested improvements in cultivation practices to limit their propagation.