Data concerning overweight and obesity in children and adolescent populations are alarming and represent one of the most serious public health problems of our time. Moreover, it is demonstrated that the school environment may play an important role in health promotion with regard to nutritional aspects. This article reports the results of a study conducted in the Apulia region (Southern Italy), aimed at providing an integrated surveillance of the behaviors related to nutrition habits in students and the hygienic and nutritional conditions of the school's canteens attended by enrolled students. To this purpose, a sample of 501 students attending primary school (third class-children approximately eight years old) replied to a validated questionnaire, and official controls (OC), of both food and nutritional safety, were performed in 22 primary schools. A team of healthcare professionals carried out the study, and the implementation of all the prescribed improvement actions were subsequently verified through follow-up OC. The results of our study show a critical situation in the student sample, with 41.3% of children having a weight excess (overweight or obesity). With regard to the children's behaviors, only 59.8% of children ate at least one fruit or had a fruit juice for breakfast, and 10.8% did not have breakfast at all. Overall, 40.1% of the total children played outdoors the afternoon before the survey and 45% reported going to school on foot or by bicycle. During the afternoon, 83.5% of the sample watched television or used video games/tablets/mobile phones, while 42.3% played sports. The schools had an internal canteen with on-site preparation of meals in 36.4%, the remaining 63.6% received meals from external food establishments. With regard to OC, for the hygienic-sanitary section, eleven prescriptions were issued, in the great part related to the structure and organization of the canteen. For the nutritional section, nine corrective actions were prescribed, mainly related to official documents and management. The follow-up OC showed that all prescriptions were subsequently addressed. Eating at school was less frequent among obese and overweight students compared with those with normal weight. Although this evidence needs to be further confirmed, it highlights the potential role that the school canteens may play in health promotion and prevention of nutritional disorders. On the other hand, in order to fulfill its health promotion task, the school canteens have to comply with official regulations and guidelines; therefore, OC during the management of the food service at school are needed.