Central Uganda has a growing number of animal shelters, particularly in urban areas, where demand for shelter services has increased due to rising numbers of stray and abandoned dogs. However, resource scarcity and overpopulation at the facilities precipitate poor physical, health and behavioural states in the dogs, lowering their adoptability. We conducted a cross-sectional animal welfare assessment study in four selected animal shelters from Central Uganda between June and August 2024 using the Shelter Quality Protocol (SQP). Key animal-based welfare issues observed were underweight body condition, diarrhoea, skin lesions, pain, fear and aggression, and stereotypic behaviours. Key shelter input factors that compromised welfare were exercise restriction, lack of pain control measures, limited veterinary care, irregular disease prevention procedures, poor feeding practices, inadequate bedding, overcrowding, and structural deficits in housing facilities. Our findings indicated that the welfare of a majority of the shelter dogs was suboptimal, limiting their chances of adoption. Addressing these concerns requires collaborating with local veterinarians, mandating strict disease prevention protocols, implementing daily dog socialization and exercise routines, and enhancing living spaces and feeding practices. Support and oversight from the government would promote improved and sustainable welfare standards in shelters.