Chemical communication in mammals is ensured by exchanging chemical signals through the vomeronasal organ (VNO) and its ability to detect pheromones. The alteration of this organ has been proven to impact animal life, participating in the onset of aggressive behaviors in social groups. To date, few studies have highlighted the possible causes leading to these alterations, and the farming environment has not been investigated, even though irritant substances such as ammonia are known to induce serious damage in the respiratory tract. The goal of this study was to investigate the environmental impact on the VNO structure. Thirty mice were split into three groups, one housed in normal laboratory conditions and the other two in confined environments, with or without the release of litter ammonia. VNOs were analyzed using histology and immunohistochemistry to evaluate the effect of different environments on their condition. Both restricted conditions induced VNO alterations (p = 0.0311), soft-tissue alteration (p = 0.0480), and nonsensory epithelium inflammation (p = 0.0024). There was glycogen accumulation (p < 0.0001), the olfactory marker protein was underexpressed (p < 0.0001), and Gαi2 positivity remained unchanged while Gαo expression was upregulated in confined conditions. VNO conditions seemed to worsen with ammonia, even if not always significantly. These murine model results suggest that the housing environment can strongly impact VNO conditions, providing novel insights for improving indoor farming systems.