Background: Primary care offers a promising setting for promoting parenting practices that shape healthy eating and physical activity behaviors of young children. This study assessed the impact of a parent-based, primary care intervention on the feeding habits, health behaviors, and body mass index (BMI) of 2–5 year olds with elevated or rapidly-increasing BMI. Methods: Four private pediatric offices in West Michigan were assigned as control (n = 2) or intervention (n = 2) sites based on patient load and demographics. Treatment families were recruited at well-child visits to receive physician health-behavior counseling and four visits with a registered dietitian nutritionist (RDN) over a 6-month period. Intervention outcomes were age- and sex-specific BMI metrics, including BMI z-scores and percent of the 95th percentile (%BMIp95), the Family Nutrition and Physical Activity survey (FNPA), and the Feeding Practices and Structure Questionnaire (FPSQ). Results: Of 165 enrolled families, 127 completed follow-up measures (77% retention). Mean (±SD) FNPA scores improved in treatment vs. control (4.6 ± 4.6 vs. 0.1 ± 4.2; p < 0.001), and screen time (h/day) decreased (−0.9 ± 1.8 vs. 0.3 ± 1.1; p < 0.001). Non-responsive feeding practices (i.e., reward for behavior (p = 0.006) and distrust in appetite (p < 0.015)) and structure-related feeding practices (structured meal timing (p < 0.001)) improved in treatment parents vs. controls. Reductions in child BMI measures did not differ between groups. Conclusions: Families with preschool children participating in a low-intensity, primary care intervention improved obesogenic health behaviors, parent feeding habits, and child screen time, but not child adiposity. Future research should assess the sustainability of these family lifestyle improvements, and evaluate their future impact on the health and development of the children.

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