The main goal of this study was to assess the impact of the economic crisis on the productivity growth of the Spanish Port System (SPS). The Malmquist Productivity Index (MPI) was estimated for the 28 Port Authorities of the SPS, for a 'non-crisis period' (2005-2008) and a 'crisis period' (2008-2011). From a policy perspective, the MPI is a very useful approach for assessing the productivity change because it can be decomposed into the catching-up index and the frontier productivity index. The results showed that the economic crisis did not impact all of the Spanish Port Authorities equally. Some Port Authorities presented higher productivity growth during the crisis period than in the non-crisis period. Further analysis by the Mann-Whitney test revealed that Port Authority investments and productivity growth were statistically related. Information provided by this study may be very useful for stakeholders and decision-makers, in terms of long-term strategic planning and improving the competitiveness of the SPS. The findings illustrate that the economic crisis should not be seen as an international tragedy, but as an opportunity to adapt port traffics and installations to new needs and market demands.