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This paper examines investment decisions regarding innovation and emissions abatement in a dynamic framework, where knowledge stock is an impure public good. We take a sector perspective based on neo Schumpeterian theory that emphasises the role of both sector and innovation systems. We interpret results taking into account sector and country based institutional, market and policy conditions. Econometric outcomes, based on an original sector dataset which exploits the NAMEA source for 15 European Union (EU) countries and 23 manufacturing sectors in the time frame 1995–2006, show that innovation efforts are positively correlated to various spillover effects. Those effects include the emissions abatement of the other sectors, thus pointing out the relevance of forces which opposite typical free riding behaviour in public or mixed public good frameworks. Different reactivity strengths for different global and local emissions also allow us to disclose the specific role of technological and economic complementarity. When considering CO2 emissions, innovation is mainly triggered by national interactions, a fact which is coherent with a dominance of national innovation and policy systems in the EU. The result is also consistent with the fact that CO2 abatement technologies heavily regard energy efficiency that provides joint private and public benefits. The fact that NMVOC abatement efforts by other sectors from abroad impact R&D investments positively means that, in some cases, a realm of sectoral systems of innovation is also relevant. The different evidence between local and global externalities is surely explained not only by the different technological and economic contents, but also by the fact that the EU has witnessed different policy implementation. [Copyright &y& Elsevier]