This article seeks to undertake a critical assessment of the changing position of public science in the entrepreneurial ecosystem of the countries on the periphery of European research. These countries are driven by new innovation paradigm based on entrepreneurship, which are implemented within the European Smart specialization strategy (S3). This article argues that S3 is widely implemented in the cohesion countries and, while it provides substantial resources for science, technology, and innovation, it fails to provide sustainability in the public research sector. This has direct implications for policies concerning innovation and entrepreneurial ecosystems. In order to prove the thesis, the article provides theoretical argumentation for emergence of a new innovation paradigm, driven by the rise of the entrepreneurial ecosystem, its incorporation into S3, and a consequent retreat of science policy in favor of entrepreneurial policy. The empirical analysis is focused on the funding trends seen in the business and public research sectors over the last decade (2008–2017), which have clearly shown that S3 has not contributed, despite expectations, to an increase in public expenditure for science. This signifies S3's neglect of public research within entrepreneurial ecosystems and challenges the ability of S3 to reduce wide disparities in research and innovation performance across the European Union. This ultimately endangers the innovation potential of the entrepreneurial ecosystem itself.