Introduction: Adequate nutrition plays an important role in linear growth throughout childhood, including puberty. However, not all children are willing or able to consume an adequate and balanced diet daily. We aimed to evaluate the 1-year effectiveness and safety of nutritional supplementation on linear growth, weight gain, and changes in body composition in short and lean peripubertal boys. Methods: A 1-year, 2-phase multicenter interventional study comprising 1-6 months of a double-blinded intervention with nutritional formula or placebo, followed by 6-12 months of an open-label extension with the nutritional formula for all participants. Results: The outcomes of the double-blinded intervention were reported previously. A total of 79/98 (81%) boys, aged ≥10 years, Tanner stages 1-3, completed the open-labeled extension phase. For this phase, a significant dose-response correlation (p < 0.05) was found of the consumption of the formula with Δheight-SDS, Δweight-SDS, and Δmuscle mass (crude correlations and after adjustment for baseline age and end-of-study Tanner stage). In the extension phase and in the 12-month analysis, participants who were good formula consumers (intake ≥50% of the recommended dose) maintained their height-SDS, while poor consumers had a significant decline in their height-SDS (p = 0.028 and p = 0.009, between group difference in the extension phase and 12-month analysis, respectively). Between-group differences were not observed in the Tanner stage at any point of the study. No serious adverse events were reported. Conclusions: An intervention in healthy peripubertal boys suggests that 1-year consumption of a multi-nutrient, protein-rich nutritional supplement is efficacious and safe. The induced changes in growth and body composition, although modest, may be clinically significant. The effect of the formula on growth parameters was not mediated by enhancement of the pubertal tempo.