Environmental impact plays a pivotal role in forming the welfare of shelter dogs exposed to chronic stress. Standard methods of animal health monitoring, such as psychological evaluation or cortisol measurements, do not fully reflect modulation of the immune system. Functional cellular changes may be subtle and observed only at the molecular level. Therefore, the aim of this study was to characterize the immune function of shelter dogs kept on different timetables in comparison with client-owned dogs. We focused on potential alterations of antigen processing by neutrophils and monocytes in animals undergoing different durations of stress. Hematological and biochemical parameters were evaluated, and changes in TLR4 and MHC Class II expression on neutrophils and monocytes isolated from peripheral blood were determined. Additionally, we measured the percentage of apoptotic cells within these leukocyte populations. Our study revealed that stressful conditions can alter the molecular pattern of surface receptors on neutrophils and monocytes, as well as the leukocytes apoptosis rate. The obtained data also indicated that the dogs' duration of stay in the shelter plays an important role in immunomodulation and triggering their adaptation mechanisms. These results bring a new perspective and will be crucial in developing improved guidelines for monitoring and promoting the welfare of shelter dogs.