Stricter energy efficiency requirements of buildings have raised concerns about their effects on indoor air quality (IAQ). We studied measured and perceived IAQ in three low-energy wooden test buildings using three ventilation levels (0.5, 1.0, and 2.0 (dm3/s)/m2). IAQ measurements included VOC (volatile organic compounds) air sampling and continuous measurements of several IAQ indicators. Perceived air quality (PAQ) was investigated with a sensory panel of untrained volunteers. The results show that the TVOC (Total VOC) concentrations were relatively low in two of the buildings already at the beginning of the study (100–141 µg/m3), and the concentrations decreased in all test buildings when ventilation was increased from the lowest level. The third building made of pinewood timber showed higher VOC concentrations (340–857 µg/m3), especially for terpene compounds that are generally present in pinewood emissions. In the PAQ assessment, the percentage of people dissatisfied (PD) with the air quality decreased with increased ventilation in all studied buildings. However, at the lowest and highest ventilation, the pinewood building had the second-lowest PD despite higher VOC levels. The findings of this study can be utilized in interpreting the effects of ventilation design and material selection on IAQ in low-energy buildings.