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This research analyzes the economic indicators of the fishery complex of the Kaliningrad region in recent years. The introduction of modern biotechnological solutions in the fish processing sector is substantiated. At present, the industry focuses on oceanic and coastal fishing, large fish complexes are leading in fish processing. Food product groups are mainly represented by chilled and frozen semi-finished products. Among food fish products, the production of sterilized canned food predominates; in smaller quantities, preserves, salted, smoked, dried and dried fish products are produced. The fish factories practically do not process fish by-products and there is no production of fish meal. To improve the economic performance of the industry, it is promising to use innovative biotechnologies and advanced foreign experience, which allow processing the extracted raw materials with maximum added value. The Strategy for the Development of the Fisheries Industry of the Russian Federation until 2030, adopted in November 2019, outlines the prospects for the development of marine biotechnology in key segments - aquaculture, production of functional and biologically active products, processing of by-products. The article presents the volumes and problems of fish by-products processing accumulating at fish processing enterprises of the region. A complex scheme of biotechnological by-products processing with the production of valuable biologically active substances (proteins, lipids, mineral substances) is proposed. The technology and production line for the production of protein, protein-mineral and lipid preparations from secondary fish raw materials are described. A modular implementation of biotechnology in marine conditions is proposed. The economic calculation from the introduction of innovative biotechnology in the processing of secondary fat-containing fish raw materials is presented.