Background <p>In Central Uganda, animal welfare advocates are increasingly promoting the establishment of animal shelters as a humane alternative to poisoning for controlling free-roaming dog (FRD) populations. However, dogs at these facilities face a number of welfare challenges arising from insufficient resources and substandard management practices. We aimed to assess the welfare of sheltered dogs in Central Uganda by identifying the animal-based welfare issues faced by the dogs, evaluating the housing and management infrastructure, and determining risk factors of animal welfare compromise. We conducted a cross-sectional study in four animal shelters, between July and August 2024. We used structured checklists from the Shelter Quality^® protocol (SQP) to collect data on animal-based measures (ABMs), resource-based measures (RBMs) and management-based measures (MBMs).</p> Results <p>Overall, the shelters housed 141 dogs (average 35.3, range 4–84) across 40 pens (average 10, range 2–17). A total sample of 32 pens were selected from which 81 dogs were assessed. Fifty-seven of the dogs were housed in groups, fourteen in pairs, and ten were housed individually. Thirty five dogs were females and 46 males. Thirty two dogs were juveniles, 41 were adults and 8 were geriatrics. The most prevalent ABMs were; ‘too thin’ body condition, skin lesions and fear/aggression, reported among 59.3%, 45.7% and 39.1% of the dogs respectively. At pen-level, signs of diarrhea, pain-associated behavior, and stereotypies were commonly seen in 46.9%, 56.3%, and 46.9% of the pens respectively. Multivariable firth’s logistic regression revealed several risk factors of poor welfare outcomes; Skin conditions, especially wounds were significantly associated with the‘other’ bedding type (aOR = 5.27, <i>p</i> = 0.008). Panting was highly associated with poorly ventilated pens (aOR = 82.33, <i>p</i> = 0.010). Pain-related behaviors in dogs were significantly linked to group housing (aOR = 11.92, <i>p</i> = 0.006), while a lack of outdoor access was a risk factor for stereotypic behaviors (aOR = 20.71, p = &lt; 0.001).</p> Conclusion <p>Our findings indicate that the welfare of the majority of shelter dogs was suboptimal, largely due to inadequate resources, poor housing conditions, and questionable management practices. Improving dog welfare in Ugandan shelters requires regulating intakes and implementing evidence-based management interventions. Collaboration with veterinary providers and intervention from animal protection agencies or government bodies can ensure sustainable, high-welfare operations.</p>