In this study we have used data from Spanish public universities to assess their efficiency in a longitudinal framework between 2008/9-2014/15. To carry out the analysis, two windows data envelopment analysis and intertemporal, non-radial and radial analysis methodologies were compared. The main results show a significant deterioration in university efficiency from the 2012/13 academic year for the three proposed frontiers, with both methodologies. Some factors may explain these results, such as the ageing of teaching force and its low replacement rate of 10%, and the lack of incentives for young researchers who wish to pursue a research career, influenced by the presence of endogamy, in hiring or promotion. Finally, the resources necessary for the good governance of the Spanish public university with the consequent accountability of these, in terms of teaching, research and its transfer to society, could become a strategic issue that should be taken into account by all the actors involved.