To assess the effectiveness of the ‘Weet wat je eet’ (‘Know what you eat’) school-based nutrition education programme on behavioural determinants and behaviour among students aged 12–15 years. A quasi-experimental study design was used, collecting data at baseline and after implementing the programme in both an intervention and control group (in total 611 students) across the Netherlands. Students from eighteen Dutch secondary education schools completed two consecutive questionnaires, assessing knowledge, self-efficacy, attitude, subjective norm, intention, and behaviours related to healthy, safe, and sustainable nutrition. Multilevel regression analyses were conducted corrected for gender, grade, education level, and school location. The intervention group showed a significant higher increase in self-efficacy, attitude, intention to drink water (all three P < 0.01), and a significant higher decrease in the consumption of sugary drinks, snacks, and meat (all P < 0.05) than the control group. Both the groups scored significantly higher on knowledge during the post-test (both P < 0.05), although the intervention group not significantly higher than the control group (P = 0.14). No significant effects were observed for subjective norm, intention, and fruit, vegetable, and whole grain bread consumption. The results of this study showed positive effects of the ‘Weet wat je eet’ school-based nutrition education programme on self-efficacy and attitude towards healthy, safe and sustainable nutrition, intention to drink more water, and various healthy eating behaviours among secondary school students. Further research is necessary to assess the long-term sustainability of these results.