Promoting a healthy diet, mainly in youths, is the most effective action to prevent and fight dietary excesses and nutritional imbalance in the population. MaestraNatura (MN) is an innovative nutritional education program aimed at promoting a healthy lifestyle in first-level secondary school students. The study evaluated the effectiveness of the MN program in improving knowledge in students following the MN program (MN group) with respect to a control group (CO group) undergoing a “traditional” nutritional education path. To this end, the nutrition knowledge of the two groups was assessed by three multi-choice questionnaires. The results showed a significant improvement in knowledge (p < 0.001) in the MN group with respect to the CO group for all the questionnaires. Furthermore, the students’ ability to transfer the principles of nutrition guidelines to the real context of daily meals was determined by asking the MN group to create a weekly food plan before (T0) and after (T1) the completion of the MN program. The MN group demonstrated improved performance in organizing the weekly menu plan at T1 with respect to T0 (p = 0.005). In conclusion, the MN nutritional education program appears to be an effective tool for improving knowledge and skills on nutritional issues, especially in those students with a lower starting level of knowledge and ability.