The aim of this study was to determine the eating habits of primary school children and to assess the nutritional value and acceptability of school menus, especially with regard to the consumption and availability of fruit and vegetables. In addition, based on the data obtained, a three-year multi-component intervention aimed at increasing children's consumption of fruit and vegetables was to be designed and implemented. 681 children from 14 primary schools participated in the study. Children's eating habits were assessed using 3-day dietary records and related to children's lifestyle habits. The quality of school meals was assessed using 2469 menus. The impact of the intervention on fruit and vegetable preference was assessed using a 5-point hedonic scale, while the impact on consumption was assessed using a food frequency questionnaire. The intervention included 23 interactive classroom workshops, 10 cross-curricular activities, 13 homework challenges, visual exposure with educational posters in classrooms, parent education via the website and the implementation of new dishes into the school food system. The results showed that less than 30% of daily school menus have adequate energy value. The average amount of fruit and vegetables in school meals varied from 20.1 ± 4.7 g to 178.8 ± 3.3 g, depending on the type and number of school meals served, which is below the recommendations for fruit and vegetable provision in school meals. At the end of the intervention, children in the intervention group increased their preferences by 0.4 and their fruit and vegetable intake by 102 g daily. The Nutri-školica intervention has been successful in changing fruit and vegetable preferences and intake among primary school children.