This paper analyzes the productivity of Swiss university departments between 1995 and 2012. Using a parametric input distance function we estimate and decompose the Malmquist productivity indexes in line with Fuentes et al. (J Product Anal 15:79-94, 2001) and Atkinson (J Bus Econ Stat 21:284-294, 2003). The adopted model is a mixed-effects model with department-specific fixed effects and random time trends. An autoregressive stochastic term is used to model inefficiency shocks with gradual dissipation by adaptation and learning. The results indicate a negative trend in Malmquist index starting from 2002, with an average rate of about 1 % per year. However, our analysis of scale effects indicates that this decline is more or less offset by universities' constant expansion and the resulting economies of scale. The results point to various patterns of overall productivity change across scientific fields that are closely related to potential productivity gains due to scale economies. In contrast to some previous studies we do not find any significant relation between productivity development and the Bologna reform.