Indoor environmental quality (IEQ) and energy conservation in schools are complex challenges. A significant part of the energy demand in these buildings addresses ventilation and temperature indoors. When confronted with money/energy constraints, the tendency of school boards is to cut on IEQ requirements, compromising the comfort of the occupants or worse, their health. Besides local energy production, either electrical or heating, major focus on Building Management Systems' (BMS) operation has been suggested, aiming at developing evidence-based energy conservation measures.Based on two field-studies, a joint approach of energy and IEQ auditing was developed, establishing a stateof-the-art of the current situation of the secondary schools in Portugal. The present study aims at enhancing energy efficiency in schools unveiling that it is possible to improve the HVAC systems' operation and optimize energy use and costs, while maintaining good environmental conditions. This paper also seeks to contribute to the implementation of Energy Efficiency Plans (EEP) in school buildings, presenting a comprehensive methodological approach on energy consumption in this typology of buildings, centered on the fundamental role of BMS and their proper programming. The obtained results show that there is a considerable potential for reducing energy consumption and improving energy usein one of the schools by simply adjusting the BMS operation schedule, a decrease between 20 -36 % of the useful thermal energy consumption is expected (14.1 -24.7 kWh/m 2 ); in other occasions, a significant IEQ improvement is expected due to longer HVAC running period.