This paper estimates relative efficiency and productive performance of 13 colleges at the University of Santo Tomas (UST), using data envelopment analysis (DEA) – Malmquist indices and a multi‐stage model. DEA is a management evaluation tool that assists with identifying the most efficient and inefficient decision‐making units (DMUs) in the best practice frontier. Total factor productivity (TFP) is measured for a sample of 13 colleges at UST over the period 1998–2003. Empirical results show that the main contributing factor to TFP growth is efficiency change. That is, UST colleges are technically operating efficiently in the frontier technology; though there is a downward shift in the technological advancement. Our results further imply that with the use of output–input mix, UST colleges as a whole have recorded a higher level of technical efficiency than innovation. These new findings contribute significantly to the existing literature on efficiency and productive performance in the education sector.