Biotechnology, defined as the technological application that uses biological systems and living organisms, or their derivatives, to create or modify diverse products or processes, is widely used for healthcare, agricultural and environmental applications. The continuity in industrial applications of biotechnology enables the rise and development of the bioeconomy concept. Bioeconomy, including all applications of biotechnology, is defined as translation of knowledge received from life sciences into new, sustainable, environment friendly and competitive products. With the advanced research and eco-efficient processes in the scope of bioeconomy, more healthy and sustainable life is promised. Knowledge-based bioeconomy with its economic, social and environmental potential has already been brought to the research agendas of European Union (EU) countries. The aim of this study is to summarize the development of knowledge-based bioeconomy in EU countries and to evaluate Turkey's current situation compared to them. EU-funded biotechnology research projects under FP6 and FP7 and nationally-funded biotechnology projects under The Scientific and Technological Research Council of Turkey (TUBITAK) Academic Research Funding Program Directorate (ARDEB) and Technology and Innovation Funding Programs Directorate (TEYDEB) were examined. In the context of this study, the main research areas and subfields which have been funded, the budget spent and the number of projects funded since 2003 both nationally and EU-wide and the gaps and overlapping topics were analyzed. In consideration of the results, detailed suggestions for Turkey have been proposed. The research results are expected to be used as a roadmap for coordinating the stakeholders of bioeconomy and integrating Turkish Research Areas into European Research Areas.