Childhood eating behaviours can track into adulthood. Therefore, programmes that support early healthy eating, including school-based nutrition education programmes, are important. Although school-based programmes may be beneficial in improving nutrition knowledge, impact on actual fruit and vegetable (FV) intake is generally limited as FV intake is also influenced by the home environment. The current study includes secondary analyses of data from an evaluation study on Dutch nutrition education and examined the role of caregivers’ health promotion behaviours (HPB) in influencing healthy eating behaviours in primary school children (n = 1460, aged 7–12 years) and whether caregivers’ HPB contribute to programme effectiveness. Children’s nutrition knowledge, FV intake and caregivers’ HPB (FV/sugar-sweetened beverages/sweets provision to take to school, cooking together and talking about healthy food at home) were measured by child-reported questionnaires at baseline, during, and 6 months post-programme. Results indicated that caregivers’ HPB was positively associated with children’s healthy eating behaviours and that programme effectiveness was highest in those in the lower HPB subcategory. In conclusion, children with less encouragement to eat healthily at home potentially benefit more from school-based nutrition education programmes than children receiving more encouragement. This highlights the important role of the home environment in supporting healthy eating behaviour in children.