Our goal was to analyse the effects of performance funding in the specific conditions of Czech and Slovak institutions of higher education, based on the assumption that the key motive for introducing performance funding is to increase accountability. The article confirms that NPM tools still co-exist with other reform trajectories and fram-ings and provides a detailed explanation of how performance funding schemes work in financing higher education-based science in selected transition countries. Finally, we observe that the effects of performance funding on accountability differ depend-ing on the funding parameters and context. We also identified forms of adaptation not previously reported in the literature.