New public management and increasing levels of competition driven by global rankings are bringing the managerial practices of public and private higher education institutions closer together. However, these two types of institutions still maintain different objectives and traditions and enjoy different degrees of autonomy that are reflected in their internal organisational structures. We study the relative efficiency and productivity performance of private and public universities in Spain through two adaptations of the Malmquist Index. Results show that, in 2009/2010, the greater flexibility of private universities meant a better adjustment between inputs and outputs in the private sector. However, in 2013/2014, public universities had caught up with private universities. Because of the economic crisis, the inputs of public universities have decreased, but this decrease had not fully impacted their results in 2013/2014.