Background: The Healthy Homes/Healthy Kids Preschool (HHHK-Preschool) pilot program is an obesity prevention intervention integrating pediatric care provider counseling and a phone-based program to prevent unhealthy weight gain among 2- to 4-year-old children at risk for obesity (BMI percentile between the 50th and 85th percentile and at least one overweight parent) or currently overweight (85th percentile ≤ BMI < 95th percentile). The aim of this randomized, controlled pilot study was to evaluate the feasibility, acceptability, and potential efficacy of the HHHK-Preschool intervention. Methods: Sixty parent-child dyads recruited from pediatric primary care clinics were randomized to: (1) the Busy Bodies/Better Bites Obesity Prevention Arm or the (2) Healthy Tots/Safe Spots safety/injury prevention Contact Control Arm. Baseline and 6-month data were collected, including measured height and weight, accelerometry, previous day dietary recalls, and parent surveys. Intervention process data (e.g., call completion) were also collected. Results: High intervention completion and satisfaction rates were observed. Although a statistically significant time by treatment interaction was not observed for BMI percentile or BMI z-score, post-hoc examination of baseline weight status as a moderator of treatment outcome showed that the Busy Bodies/Better Bites obesity prevention intervention appeared to be effective among children who were in the overweight category at baseline relative to those who were categorized as at risk for obesity (p = 0.04). Conclusions: HHHK-Preschool pilot study results support the feasibility, acceptability, and potential efficacy in already overweight children of a pediatric primary care-based obesity prevention intervention integrating brief provider counseling and parent-targeted phone coaching. What's New: Implementing pediatric primary care-based obesity interventions is challenging. Previous interventions have primarily involved in-person sessions, a barrier to sustained parent involvement. HHHK-preschool pilot study results suggest that integrating brief provider counseling and parent-targeted phone coaching is a promising approach.