Stakeholders and their dynamics are often neglected in innovation systems literature. The importance of bioeconomy is growing for its implications on addressing environmental challenges, shaping economic decisions, markets and sustainable development. This paper analyses stakeholders’ dynamics for knowledge creation and innovation to transit from unsustainable practices to the sustainable use of biological resources - bioeconomy. The originality of this paper is the creation of an analytical framework to characterise the interactions of stakeholders and how these interactions reshape the innovation systems to create a new narrative and a new knowledge base platform for innovation. Using a qualitative approach, data was collected through surveys between 2022 and 2024. We explored the dynamics of 29 stakeholders involved and collaborating in R&D activities from the biotechnology sector in Caldas, Colombia. Our findings show that dynamics towards bioeconomy are only at the discursive level. Stakeholders carry out research activities as a means to generate income rather than for innovative purposes, overlooking informal interactions which generate novel ideas that could translate into solutions, services, and products. We conclude that bioeconomy transition needs a systemic disequilibrium by a new institutional infrastructure that enables stakeholders, including civil society, to create a structural change for embracing innovation dynamics.