The article explores the organisational impact of evaluation and control mechanisms on universities from the point of view of accountability. Three case studies are analysed with the aim of understanding the significance of these systems both at corporate governance level and in relation to their influence on the behaviour of the academic staff. Open-ended, in-depth interviews were conducted in three universities from two countries in order to collect the opinions of the top managers and academics with different roles and seniority. The combination of four different but partially overlapping analytical frameworks (new public management, neo-institutional sociology, organisational control theory and sense-making) has supported the analysis and the interpretation of the empirical material collected. The analysis sheds light on a somewhat neglected aspect: the interdependence among various systems and tools that simultaneously operate in an organisation and inevitably combine to influence the behaviour of its employees. On this basis indications are given in order to facilitate the introduction and the management of more appropriate evaluation mechanisms both at the national system and the organisational level.