Biological transformation represents one of the most promising optimization strategies for a sustainable economy. The rapid convergence of biotechnology, information technology and production technology provides a vast area of innovation. From an economic and innovation policy perspective, cooperation structures and value creation systems will change significantly in a biointelligent transformation process. In the future, many industries will produce personalized products in a much more decentralized manner based on locally provided, renewable resources using autonomous non-expert systems. Such a profound change affects not only products and processes but also the organization of companies and how innovations are evaluated and implemented. In this paper, we thus discuss the need for a reorientation of innovation management in companies in the context of biological transformation. This article focused the central question of how the innovation management can change in the context of biointelligence so that companies can be helped to invest strategically in biointelligent innovations. We then outline the basic elements of a framework and discuss key challenges for future research and development. In this paper, we present initial thoughts on a framework for the management of biointelligent innovation that aims to solve the complex requirements of BioIntelligence. Our approach is based on a holistic view of different methods and techniques to provide a comprehensive solution to the challenges. We discuss the basic concepts and goals of this framework as well as potential application areas and challenges. Furthermore, we present first approaches for implementation and evaluation.