This article examines how knowledge transfer (KT) indicators affect analyses on efficiency in the Higher Education sector, taking into account the characteristics of the Higher Education Institutions (HEIs). After revising the concept of third mission as a field for data development and its importance in assessing university performance, we applied various data envelopment analysis models with different specifications to 47 Spanish public universities to test whether KT indicators are relevant when evaluating the performance of HEIs in terms of their efficiency and, if so, which indicators are most suitable. Our results suggest that the effect of including KT indicators in the efficiency analyses varies from university to university according to their characteristics. The subject mix taught at the university, the focus according to each mission's relative importance within the total range of activities carried out in each university (mission mix), and the mix of their third mission activities affect the increase of the universities' efficiency scores when KT is taken into account in the analysis. This means that these factors affect the universities' position for the different efficiency scores.