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Immobilization of microalgae cells (MA) facilitates their harvesting constituting a major challenge in algal biotechnology. Increased cell density, lower risk of contamination, and higher resistance to various stresses can enhance immobilized MA productivity regarding valuable metabolites as compared with the corresponding suspended cultures. The chlorophyte strain Lobosphaera sp. IPPAS C-2047, which is the prospective candidate for the efficient phototrophic production of arachidonic, linoleic and α-linolenic acids, served as the object in the present work. The solid, highly porous and hydrophilic polyethylenemine (PEI) and chitosan-based polymers (CH), synthesized by method of cryopolymerization with diethylene glycol diglycidyl ether and glutaraldehyde, were tested as the MA carriers. The profound difference of the effect of immobilization on PEI and CH on lipid metabolism of Lobosphaera sp. was revealed. The immobilization on PEI increased ARA percentage in the total tatty acids and ARA volumetric productivity by 72% and 81%, compared with the suspended cells cultured respectively in complete or nitrogen-deprived medium 14 days. Immobilization on CH declined ARA but increased oleic and α-linoleic acid percentages. Importantly, total volumetric FA content in the cells immobilized on both carrier types was 15–35% higher than that of the suspended cultures regardless of nitrogen availability. In view of the advantages of attached cultivation, immobilization of Lobosphaera sp. IPPAS C-2047 on the CH- and PEI-based polymeric cell carriers is a promising avenue for the development of viable technology for increasing of polyunsaturated fatty acids productivity yield and especially, productivity of Lobosphaera towards the arachidonic, linoleic and α-linolenic acids.