Notwithstanding a recent upsurge in interest in knowledge intermediaries and their roles in innovation support systems, we know little about the interplay between the activities of academia-driven intermediaries and their publicly financed counterparts. Building on a combination of principles derived from the resource-based theory and entrepreneurial ecosystems literature, this paper investigates the potentials of cooperation between different knowledge intermediaries. Therefore, the authors analyze the alignment of financial, knowledge, market and network resources in politically funded regional alliances between university-internal and university-external intermediaries by means of a qualitative approach. They find that, while knowledge intermediaries can benefit from access to additional ecosystem-specific resources, the urge to improve their own position within the ecosystem hampers the will to cooperate and can lead to non-performing resource alignments. The paper contributes to current scholarly discussions by suggesting and testing a theoretical foundation for analyzing the cooperative behavior of knowledge intermediaries in innovation support systems.