Selenium nanoparticles are attracting the attention of researchers due to their multiple applications, including medicine. The biosynthesis of selenium nanoparticles has become particularly important due to the environmentally friendly character of the process and special properties of the obtained particles. The possibility of performing the biosynthesis of selenium nanoparticles via the living culture of Arthrospira platensis starting from sodium selenite was studied. The bioaccumulation capacity of the culture, along with changes in the main biochemical parameters of the biomass, the ultrastructural changes in the cells during biosynthesis and the change in the expression of some genes involved in stress response reactions were determined. Protein, lipid and polysaccharide fractions were obtained from the biomass grown in the presence of sodium selenite. The formation of selenium nanoparticles in the protein fraction was demonstrated. Thus, Arthrospira platensis culture can be considered a suitable matrix for the biosynthesis of selenium nanoparticles.