The transition to a sustainable bioeconomy by a customized approach would speed up its development and make it more targeted. There is still no common international method for determining, measuring and comparing the extent of sustainability. The aim of this research is to develop a methodology for the assessment of bioeconomy-influencing factor interlinkages, and creation of benchmarks through a top-down approach. The main output is the assessment of factor interlinkages that could be further used for composite index creation. A case of triple factor nexus is presented: policy, research and innovations, and technology nexus for EU countries. As a result, the empirical model presents the mathematical description of policy, research and innovation, and technology link benchmark.