The Bologna reform aims to enhance several dimensions of the universities' activities, by favouring mobility and mutual recognition of higher education degrees across Europe, with the objective to create a European Higher Education Area. The radical changes induced by the Bologna Process affect universities' productivity both directly (for example, implementation costs, curriculum streamlining, evaluation intensity) and indirectly (for example, the ability to attract more students and higher levels of competition among institutions). The decentralised organisation of the Swiss university sector provides an ideal setting to test this hypothesis, as the panel data of departments permits the consideration of the unobserved heterogeneity across both universities and scientific fields. The empirical results support the claim that the Bologna reform enhances university productivity. Furthermore, there is no evidence of substantial costs of the system transformation.