Weight and body mass index (BMI) changes appear to be poor measures for assessing the success of most pediatric obesity prevention programs (POPP). The aim of this study is to evaluate the effectiveness of the preschool-age prevention program (3P) in improving and maintaining overtime preschoolers’ knowledge/preferences about healthy nutrition and physical activity (PA), and the relationship between acquired healthy behaviors and anthropometrics including waist circumference (WC). Twenty-five preschoolers underwent a 24-month healthy lifestyle multi-component pilot intervention followed by a one-year wash-out period; 25 age-matched served as controls. Anthropometric/behavioral data were monitored. After the 2-year study and wash-out, the rates of children overweight and with obesity decreased only in the intervention group, where, also, normal-weight children with visceral obesity attained WC normal values (p = 0.048). While mean values of BMI Z-scores remained unchanged in both the intervention and control groups, WC (values and percentiles) showed a significant reduction only in the intervention group. Children’s adherence to the Mediterranean diet remained acceptable among the entire sample. Although daily sweet beverage consumption remained unchanged in both groups, knowledge/preferences improved significantly more in the intervention group. In conclusion, WC may be more sensitive than BMI for monitoring preschoolers in POPP and reflects healthy behavioral changes acquired during the intervention.