Every type of bio-resources has its specific and multi-tier applications. To promote resource efficiency and complete use of bio-resources the simplistic and environmentally less valuable options must be replaced with technological solutions that contribute to development of high added value products, while ensuring environmental sustainability. This paper proposes a methodology for evaluation of the added value of various bio-resource applications in order to optimize the use of bio-resources. The optimization target function is determination of net present value depending on product price and its growth, economic feasibility, product sustainability, specific water and energy consumption, operation and maintenance parameters. The methodology incorporates a system of equations that describe the product value and the required investments at each level of applications. Simultaneously, the impact of bio-resource application and the developed product on climate change is evaluated. The developed methodology is approbated for identification of technological opportunities of quince by-product valorisation. Comparison of four alternative scenarios proves the applicability of the optimization method and determines that the highest net present value and the lowest CO2 emissions would be for a case of quince seed oil extraction at the facility of existing food processing company.