The present study aimed to evaluate animal welfare of pigs from the same farm, raised with two ventilation systems. The study involved 60 pens of fattening pigs, raised in two buildings: one naturally ventilated (NV) and the other mechanically ventilated (MV). Pigs were assessed on three observation days: at 40 kg (T1), 100 kg (T2), and 160 kg (T3) of live weight. Animal-based measures were used such as qualitative behavioral analysis (QBA), behavioral measures (BMs), and lesion and health measures (LHMs). Housing conditions (HCs) measured at each observation day were the number of pigs per pen, space allowance, temperature, light, and CO2. The association study was performed using a general linear model and analysis of variance. Ventilation effect was analyzed by performing computational fluid dynamics. Results showed that overall pigs raised in the MV were in a more positive affective state. Despite that, with hot temperatures, the higher occurrence of pig soiling indicated heat stress in pigs and consequent welfare impairment. The higher frequency of pigs showing dog sitting behavior at T2 and T3 suggest welfare worsening in the last phases of fattening. The study concludes that ventilation system influences animal behavior and overall animal welfare, especially during the warmer season.