As an integral part of the EU’s Green Deal, the purpose of the bioeconomy is to ensure an effective transition to meet people’s needs based on renewable resources while maintaining economic growth. This study undertakes the modeling of bioresource value scenarios in the agricultural sector and proposes a methodology to evaluate the possibilities of reaching a higher added value of bioresource products. The main objective of the study is the adaptation of the market allocation–energy flow optimization model system (TIMES) for analysis of high-value-added product production capacities in the livestock sector to reach an increase in added value for 2030 with the introduction of new technologies. The developed model is tested in a case study of the animal husbandry sector in Latvia. The results show which pathways are economically feasible to achieve value-added targets set for 2030. Although not all of the available resources are used due to local market limitations, there is significant potential for the use of animal husbandry resource waste, and it is possible to achieve about 62% higher cumulative added value from 2023 to 2030 with the production of new products (protein powder, wool pellets, and gelatin) in comparison with the base scenario.