Based on a disaggregate cross-country analysis, we investigate the performance of 10 public Swiss universities and 77 public German universities from 2001-2007. During this period the universities in both countries have faced two major reforms aimed at improving efficiency and productivity in the European higher education sector. We assess the change in productivity and its sources, that is technological change, technical efficiency change and scale effects, obtained by computing the non-parametric Malmquist productivity index by benchmarking the non-science disciplines and the science disciplines of both countries separately against a common frontier. Given the lack of statistical inference of non-parametric productivity analyses, we employ bootstrapping techniques and estimate confidence intervals, allowing us to verify the statistical significance of our results. The results indicate that improvements in technical efficiency were by far the most important driver for productivity growth, followed by gains realised through exploiting economies of scale; thereby technological change partly reduced the increases in productivity. Our findings, however, suggest reform-related differences between the Swiss and the German public university sector. Further, the results point to structural differences across the scientific disciplines, as we found divergent patterns for the development in productivity and its sources in the non-sciences and the sciences.