<p>Core firms face the challenge of building and aligning internal processes with the evolving nature of innovation ecosystems to sustain their position as ecosystem leaders. Yet, we know little about the process by which core firms align their internal processes with innovation and knowledge ecosystems to generate valuable innovations. How do core firms align internal processes (i.e., innovation processes and knowledge transfer) when engaging with different types of ecosystems? Building on the literature of co-evolution, we address this question through an in-depth single-case study of a leading aircraft manufacturer that engaged with multiple local and global knowledge ecosystems to create, develop, and improve multiple innovation ecosystems over time. By employing a processual approach to analyze 51 interviews and multiple sources of secondary data from managers within the core firm and the knowledge ecosystem, our theorization reveals the unique mechanisms through which core firms navigate the challenges of co-evolution. Our main contribution is the proposal of a new framework for twin ecosystem alignment, comprising three distinct phases: engaging, catalyzing, and orchestrating. The article contributes to the ecosystem management literature and the university-industry collaborations literature by theorizing how a core firm utilizes unique processes to co-evolve internal processes with different ecosystems over time. We also contribute to managers involved in orchestrating innovation and knowledge ecosystems by offering a processual account of how firms navigate the co-evolution challenges that emerge throughout this process. Our study offers initial empirical guidance for managers responsible for orchestrating both the innovation ecosystem and the knowledge ecosystem.</p>