The early introduction of effective nutritional educational programs is pivotal for instilling sustainable healthy behaviors. The present work aims to present a best practice example of a nutrition and overall lifestyle school-based training program, the Nutritional Adventures (“Diatrofoperipeteies”). Conducted during 2020–2022 in Greek primary schools, this synchronous, online educational initiative included two 1-school-hour activities with a nutrition instructor. Additionally, schools were randomly assigned to supplementary “at-home” supported-by-parents or “in-class” supported-by-educators educational activities. In total, n = 12,451 students of 84 primary schools participated. Parent-completed questionnaires were selected in the recruitment and post-intervention phase (40% participation rate); overall, the working sample was n = 1487 students. In the post-intervention phase, a significant increase in Mediterranean diet adherence was observed (KIDMED score: mean increment = 0.25 units; p < 0.001), particularly fruit and vegetable consumption. Time spent on physical activity increased, while screen time decreased. Students’ total quality of life significantly improved (PedsQL; mean increment = 1.35 units; p < 0.001), including on all of its subscales (physical, emotional, social, and school function). Supplementary educational activities that were supported by educators rather than parents yielded a more favorable impact on students’ lifestyle and quality of life. The Nutritional Adventures program can be regarded as a successful initiative in primary schools, yielding immediate advantages that extend beyond promoting healthy dietary habits.