This study proposes an innovative two-sta-ge approach, using Data Envelopment Analysis and Biplot, to evaluate the techni-cal efficiency of 30 academic departments of a Chilean university, and to identify the main factors affecting their performan-ces. Public higher education worldwide is under a growing pressure to increase efficiency and improve the quality of edu-cation with limited governmental funds given to state-owned universities. The ri-gorous supervision and regulations make the use of decision-making approaches for the rationale administration of financial resources imperative. The first stage used an output-oriented DEA model, using 3 con-figurations under the assumption that the units under analysis have more influence on producing outputs than on generating income. The second stage employed a Bi-plot analysis to characterize the depart-ments into four clusters, and to identify external variables influencing the (in)effi-ciency scores. Results indicated that acade-mic departments focused on teaching are more efficient than those aiming for re-search. Among the main factors affecting the level of performance were the num-ber of full-time equivalent faculty holding graduate studies, and the average course approval ratio.