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Tools for Smart Specialisation Strategy (RIS3) development to assess at which territorial level innovation is concentrated and how innovation systems compare across regions and sectors remain scarce. The triple helix indicator is a data-driven tool that can serve in RIS3 development to assess synergy in innovation systems based on readily available data sets. For Germany, we find strong decentralization with innovation system synergy concentrated at regional and local levels. Innovation systems in manufacturing are less regionalized than in knowledge-intensive services. An East–West divide persists. RIS3 policy-making should account for decentralization by building capacity for region-specific RIS3 development at lower governance levels.