The use of various types of functional non-traditional plant and animal raw materials in the preparation of bakery products is a classic approach to increasing their biological and nutritional value and requires the use of mathematical methods for designing recipes. The paper presents the results of modeling the composition of bakery products with amino acid and fatty acid composition recommended by the Federal Research Center for Nutrition and Biotechnology, close to the reference value of an ideal protein. An analysis of the biological value and biological effectiveness of plant functional raw materials (flax seeds, sesame and pine nuts) was carried out in order to enrich them with new products for the baking industry. A mathematical optimization problem was formulated and, using the Maple computer algebra software environment, the optimal ratio of components was calculated to ensure the maximum approximation of the biochemical composition in terms of the ratio of essential amino acids, as well as ω-6 and ω-3 polyunsaturated fatty acids, to the reference value in the developed bakery products. The ratios of new components used in the recipe provided an increase of 31.4% in the biological value and a decrease in the energy value of the developed bakery products by 3.8%. The finished product is balanced according to the ratio ω-3: ω-6 = 1.0: 3.9 and mineral substances Ca: P: Mg = 1: 1.49: 0.6. Satisfaction of the daily requirement for functional ingredients is 21 - 31% (in control - 14%). The results obtained and the proposed methodology can be used as a model for enriching the composition of various functional foods.