Mixed methods research is interesting to understand complex processes. Organ transplants are complex processes in need of improved final performance in times of budgetary restrictions. As the main objective a mixed method approach is used in this article to quantify the technical efficiency and the excellence achieved in organ transplant systems and to prove the influence of organizational structures and internal processes in the observed technical efficiency. The results show that it is possible to implement mechanisms for the measurement of the different components by making use of quantitative and qualitative methodologies. The analysis show a positive relationship between the levels related to the Baldrige indicators and the observed technical efficiency in the donation and transplant units of the 11 analyzed hospitals. Therefore it is possible to conclude that high levels in the Baldrige indexes are a necessary condition to reach an increased level of the service offered.