This study investigates the prevalence of Canine Parvovirus (CPV) and Canine Coronavirus (CCoV) among shelter dogs in Portugal. Despite advancements in veterinary medicine and widespread vaccination efforts, CPV and CCoV continue to pose significant health threats to the canine population, particularly in high-density environments such as shelters. Through a cross-sectional study involving 240 shelter dogs in five municipalities in Portugal, this study utilised an immunochromatographic technique for the simultaneous detection of CPV and CCoV antigens. The findings reveal a 6.2% and 9.2% prevalence of CPV and CCoV, respectively, with a co-infection prevalence of 4.6%, highlighting the persistent challenge these viruses represent. The study further explores the lack of significant association between infection prevalence and variables such as age, sex, breed, and municipality, suggesting that susceptibility to these infections may be broadly distributed among shelter dogs. By providing new insights into the epidemiology of CPV and CCoV within Portuguese shelters, this study contributes to the body of knowledgenecessary for developing targeted strategies to manage and prevent these infectious diseases in high-risk canine populations.