•An intervention programme was designed to teach children healthy diet and habits.•A new web app called “¿Cómo como yo?” (How do I eat?) was used.•Food neophobia score and healthy habits were compared among two European countries.•The intervention reduced food neophobia and improved children healthy food habits.•The success of the intervention was related to childreńs food neophobia score. Healthy eating patterns in childhood promote optimal childhood health, growth and intellectual development. In this context, effective educational programmes to promote healthy eating habits during childhood are needed specially in countries where childreńs overweight and obesity are becoming a serious problem. The main aim of this study was to test the effectiveness of a full healthy eating intervention programme focused on the improvement of healthy habits of children from two European countries (Poland and Spain). For achieving this objective, a new web app named “¿Cómo como yo?” (How do I eat?) especially designed for school-aged children was used for collecting the data and for making recommendations of healthy eating habits after the questionnaires were completed. Although 407 Polish and Spanish primary school pupils completed the intervention, after data curation, 339 of them were included in the study. Our results showed that the educational intervention was useful to decrease food neophobia in children and to increase some healthy habits. The success of the healthy eating intervention programme was related to childreńs food neophobia score. The results allowed us to describe country-related differences in food neophobia, food acceptability, food habits and healthy knowledge. Finally, the healthy eating intervention programme has proved that a change in children eating behaviour is possible. In fact, our findings have implications for formulating several recommendations for educational programmes in different EU countries.