Fish-derived lipids have a high carbon potential, containing unique long-chain and polyunsaturated fatty acids. They are an effective lipid substrate for the microbial synthesis of industrial biotechnological products. The aim of this study was to analyze methods for extracting lipids from secondary fish feedstock, investigate their quality indicators, and justify their use in the biotechnological synthesis of proteins and biodegradable plastics.Lipids were extracted using three methods: thermal, enzymatic, and a combined ultrasound approach. The fat fractions were analyzed for their recovery rate, impurity content, hydrolytic and oxidative degradation, and fatty acid composition. The best yield and quality of fat were achieved with enzymatic extraction. Using the enzyme Alcalase, larger batches of fat were produced from smoked sprat and mackerel heads. A higher level of fatty acid preservation was established in sprat lipids compared to mackerel lipids, based on acid, peroxide, thiobarbituric, and anisidine values.The fatty acid composition of the lipids demonstrated their high biological value in all batches. Increased levels of unsaturated (67-69%), long-chain (29-51%), and polyunsaturated (27-32%) fatty acids were observed, including eicosapentaenoic and docosahexaenoic acids of the omega-3 family (25-26%). At the Institute of Biophysics of the Siberian Branch of the Russian Academy of Sciences, single-cell proteins and biodegradable polyhydroxyalkanoates with high technological properties were synthesized using large batches of fish oils as substrates.