This study examines the effectiveness of the peer-delivered, school-based intervention Healthy by Design (HbD). Data were collected in two cross-sectional surveys before and after invention implementation. In total 1,177 vocational students (before: 557, after: 620) participated in an online health behaviour survey. Multilevel logistic and multilevel linear models explored the effect of the intervention over time and the effect of the intervention dose received on (determinants of) dietary of physical activity behaviours. A significant positive effect over time was found for moderate intensity physical activity. A high intervention dose was positively associated with increased water, breakfast and fruit consumption and higher levels of moderate and vigorous physical activity compared to no intervention dose received. A moderate and high intervention dose was negatively associated with high calorie snacks consumption compared to no intervention dose received. Effects of HbD on the investigated dietary and physical activity behaviours over time are limited, but these effects may be hard to demonstrate and link to the intervention due to the nature of the intervention design and the natural school-setting of this quasi-experimental study. However, a higher intervention dose showed a strong relation with healthier dietary and physical activity behaviours.