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The creation of new effective biotechnologies for the sustainable use of nutrient is necessary to maximize the reuse of N and P in the production of fertilizers and protect the environment from eutrophication. Immobilization of microalgae (MA) on carriers is a promising approach facilitating the harvesting of MA biomass and protecting the cells from unfavorable environment. The synthesis of composites on the basis of chitosan (CH) and polysaccharides-containing waste (PCW) of food, biotechnological and textile industries is a prospective approach in terms of low cost, low emission and sustainability. The chlorophyte strain Lobosphaera sp. IPPAS C-2047 served as the object in the present work. We tested composites obtained by cryopolymerization of CH, apple pomace (AP) and mushroom mycelium (MM), which are the main by-products in the apple juice processing industry and in mushroom farming. A CH solution and AP or MM suspensions in 2% (w/w) acetic acid were mixed in 1:3, 1:1 or 3:1 ratio, cross-linked with glutaraldehyde and freeze-dried to prepare porous and solid composite sponges. Comparison of composites sorption efficiency towards model culture Lobosphaera demonstrates that the addition of 25%, 50% of MM results in significant increase of the attached MA number, while the immobilization efficiency of composites with 25%, 50% of AP and additive-free CH was similar. The tested composites supported the prolonged cultivation of immobilized MA without impairing their growth and photosynthetic activity. The nutrient removal capacity of immobilized Lobosphaera cells was higher as compared to that of the suspended cells. Collectively, the biodegradable and non-toxic chitosan-based composites were shown to be environment-friendly materials providing the enhancement of nutrient bioremoval from wastewater by immobilized MA.