Children with disabilities have higher prevalence estimates of obesity than typically developing children. The Healthy Caregivers–Healthy Children Phase 3 (HC3) project implemented an obesity prevention program adapted for children with special health care needs (CSHCN) that includes dietary intake and physical activity (PA) components. The primary outcome was a change in dietary intake, PA, and the body mass index (BMI) percentile. Ten childcare centers (CCCs) serving low-resource families with ≥30 2- to 5-year-olds attending were randomized to either the intervention (n = 5) or control (n = 5). The HC3 CCCs received (1) snack, beverage, PA, and screen time policies via weekly technical assistance; (2) adapted lesson plans for CSHCN; and (3) parent curricula. The control CCCs received a behavioral health attention curriculum. HC3 was delivered over three school years, with data collected at five different timepoints. It was delivered weekly for six months in year one. To ensure capacity building, the HC3 tasks were scaled back, with quarterly intervention delivery in year 2 and annually in year 3. Adaptations were made to the curriculum to ensure appropriate access for CSHCN. Given that the program was being delivered during the COVID-19 pandemic, special modifications were made to follow CDC safety standards. The primary outcome measures included the Environment and Policy Assessment and Observation (EPAO) tool, standardized dietary intake and PA assessments, and the child BMI percentile. CCCs are an ideal setting for targeting CSHCN for obesity prevention efforts as they provide an opportunity to address modifiable risk factors.