Drawing on the systems perspective of innovation processes, this article proposes a conceptual approach for a comprehensive analysis of regional knowledge generation and transfer. Instead of focusing on one single indicator, the approach emphasises the importance to take multiple channels of knowledge transfer into account. This provides valuable insights into the spatial structure of innovation processes on different levels. We disentangle the innovation process and consider four different layers: 1publications in peer-reviewed journals 2patent applications 3formal R&D collaboration projects 4localised input-output relations. Further, we demonstrate the relevance of the ‘multi-layer approach’ by applying it empirically to a specific regional innovation system: The Free State of Saxony – a federal state in Germany. We argue that the approach could be a valuable tool to inform policy makers about knowledge-based regional development strategies.