In addition to promoting reforms, governments foster change in university systems through funding, competition, and new policy instruments. Little research has been conducted on how research centre funding schemes support organizational changes in universities and on their institutional and policy barriers. This article addresses the research centre funding schemes implemented by the regional government of Galicia (Spain) in 2016. The approach is observational and based on documentary analysis and semi-structured interviews with key actors. The regional government sought to encourage organizational differentiation by increasing the autonomy of centres inside the universities and to enhance strategic research agendas, reinforcing the scientific authority of the centres’ directors. We found that the design and operation of the instrument in the context of the existing university governance system, and the interaction with other funding instruments within the policy mix, may create barriers that hinder the effectiveness of the funding scheme.