The biological transformation of added value is seen as one of the key aspects in applied research. Bioinspired methods and technologies will affect factories of the future and enable them to cope with changing boundary conditions and the rising necessity of sustainability. This results in a higher demand for flexibility and transformation ability of the comprised production systems. To elaborate topics like these, Fraunhofer initiated strategic collaborative research projects. The current project aims at developing aspects of the biological transformation, whereof organic bio-inspired factories is one. Different research focal points were identified as enabling technologies on different levels of the well-established automation pyramid. The paper highlights the aspects “facility layout planning”, “behavioral modeling of production systems” and “skill-based controller programming” as enabling technologies. Solution approaches for the addressed aspects are discussed and future steps towards a flexible and sustainable production are shown.