Party politicization of the public administration was a core feature of the state-socialist systems of Central and Eastern Europe. Nevertheless, many studies agree that the practice continued and even thrived after democratization and is still among the most important features of post-socialist politics. This paper connects the debates on post-socialist party politicization and the absorption of EU funds in order to account for new member states’ problems to use their EU funds in the 2007-2013 financing period. It formulates a causal mechanism for low absorption based on the politicization of the planning and staffing process of cohesion policy implementation. The mechanism is tested in two process tracing case studies in the Czech Operational Programme Environment and the Romanian Operational Programme Transport. The case studies are based on both document analysis as well as a multitude of interviews with different actors conducted during five distinct field trips to the region. Despite of the large differences between both countries and programmes, it is suggested that the same mechanism of party politicization and regular alternation on the level of ministries causes in both cases serious absorption problems.