This paper evaluates the performance of the foundation sector in Spain by applying the non-parametric technique of Data Envelopment Analysis (DEA), proposed by Charnes, Cooper, and Rhodes (1978) and Banker, Charnes, and Cooper (1984). The study is based on a sample of 172 Spanish foundations, framed inside the sub-sectors of care and educational–cultural foundations, both of them relevant in the national foundation sector. In order to measure the performance of these kind of non-profit organisations, we designed a model based on the economic and financial information obtained from the annual accounts for the period 2008–2010. We classified the sample according to the different types of foundations and applied the technique known as programme decomposition approach (Charnes, Cooper, & Rhodes, 1981) to determine which foundational model achieves a better management performance. Subsequently, the work was completed with the two-stage DEA analysis to evaluate the main factors that determine the management performance of these entities for the period of study.