A comprehensive assessment of indoor environmental conditions is performed on a representative sample of classrooms in schools across southern Spain (Mediterranean climate) to evaluate the thermal comfort level, thermal perception and preference, and the relationship with HVAC systems, with a comparison of seasons and personal clothing. Almost fifty classrooms were studied and around one thousand pool-surveys distributed among their occupants, aged 12 to 17. These measurements were performed during spring, autumn, and winter, considered the most representative periods of use for schools. A new proposed protocol has been developed for the collection and subsequent analysis of data, applying thermal comfort indicators and using the most frequent predictive models, rational (RTC) and adaptive (ATC), for comparison. Cooling is not provided in any of the rooms and natural ventilation is found in most of the spaces during midseasons. Despite the existence of a general heating service in almost all classrooms in the cold period, the use of mechanical ventilation is limited. Heating did not usually provide standard set-point temperatures. However, this did not lead to widespread complaints, as occupants perceive the thermal environment as neutral—varying greatly between users—and show a preference for slightly colder environments. Comparison of these thermal comfort votes and the thermal comfort indicators used showed a better fit of thermal preference over thermal sensation and more reliable results when using regional ATC indicators than the ASHRAE adaptive model. This highlights the significance of inhabitants’ actual thermal perception. These findings provide useful insight for a more accurate design of this type of building, as well as a suitable tool for the improvement of existing spaces, improving the conditions for both comfort and wellbeing in these spaces, as well as providing a better fit of energy use for actual comfort conditions.