The need for energy-efficient buildings must be based on strong effective passive-design techniques, which coordinate indoor air quality and thermal comfort. This research describes the principles, simulation, implementation, and monitoring of two different natural cross-ventilation algorithm scenarios applied to a school-building case study affected by a subtropical climate during the winter season. These ventilation protocols, the steady and dynamic versions, can control the carbon dioxide concentration and actuate the window openings according to pre-defined window-to-wall ratios. The implementation of the monitoring process during three non-consecutive days in the winter of 2021 validates the opening strategy to maintain carbon dioxide below 800 ppm, described by the protocol Hygiene Measures Against COVID-19, and the temperature within the comfort ranges suggested by the adaptive UNE-EN 16798. The study shows that a steady opening of 2.16% window-to-wall equivalent ratio can be enough to maintain the requested comfort and carbon dioxide conditions. The use of the dynamic window ratios, from 0.23% to 2.16%, modified according to the measured carbon dioxide concentration, can partially maintain the carbon dioxide below the required limits for ASHRAE 62.1, Hygiene Measures Against COVID-19 and UNE-EN 16798 between 48.28% to 74.14% of the time. However, the carbon dioxide limit proposed by RITE, 500 ppm, is only achieved for 15.52% of the time, which demonstrates the inadequacy of the natural ventilation to fulfil the standard. Further improvements in the dynamic control of the openings in these buildings could lead to lower carbon dioxide concentrations while maintaining the thermal comfort in mild winter climates.