This policy paper analyses current practices related to the implementation of European Structural and Investment Funds (ESIF) in the Slovak Republic, in particular, the Operational Programme Research and Innovation (R&I). The Slovak Republic benefits from one of the largest shares of European Structural and Investment Funds (ESIF). However, the country ranks amongst the EU member states with the lowest absorption of R&I ESIF. In 2017, administrative inefficiencies and irregularities resulted in further decommitments by the European Commission. This paper identifies bottlenecks in the ESIF projects’ implementation across the entire project life cycle, from the preparation of calls to the execution of selected projects. It offers the Slovak Republic tailored policy recommendations to support the effective implementation of European funds for research and innovation and avoid further decommissioning. To ensure lasting changes, this policy paper proposes an action plan where all relevant stakeholders would contribute to effectively implementing transformational reforms.