In recent years, wooden frame structures have become increasingly popular. As in any usable space, indoor air quality is essential. Appropriate parameters in the indoor environment are necessary for healthy and comfortable use. It is especially crucial for residential buildings where occupants rest and sleep, assuming the air quality is acceptable. Prefabricated energy-efficient construction in a wooden frame structure brings many benefits. These are modern buildings, and the solutions used ensure utility benefits and cost efficiency. This paper presents a comprehensive assessment of the performance of mechanical ventilation systems in energy-efficient, prefabricated timber frame buildings, focusing on indoor air quality (IAQ), thermal comfort, and energy efficiency. Three single-story family houses, each approximately 90m2, were studied in different locations in southern Poland. The analysis included measurements of air flow rates, CO2 concentration, humidity, temperature, and sound levels within these buildings. The ventilation systems, equipped with an air handling unit with heat recovery, were analyzed. It was found that the ventilation systems allow for appropriate air exchange, effectively managing indoor climate despite external temperature variations. Results indicate that the timber frame construction combined with advanced ventilation systems provides significant benefits in maintaining IAQ and thermal comfort while adhering to energy efficiency standards. The study highlights the importance of integrating mechanical ventilation with heat recovery to achieve optimal performance in low-energy buildings.