The high prevalence of overweight among children and adolescents has led to an increase in school-based prevention programmes. The aim of the present paper is to present the concept of an initiative called "BEO'S" as well as the experience made with the implementation und acceptance of this programme in the participating schools. Different from the majority of school-based projects for healthy eating and physical activity, BEO'S pursues a systemic approach that includes the whole school and is tailored to the school's respective resources. Characteristics are (1) the participation of teachers, students, parents, and caretakers, (2) the motivation and empowerment of schools to plan and implement activities by themselves, (3) the focus on environmental approaches, and (4) addressing and considering the individual school's needs and resources. The university project team supports the schools by individual counselling as well as providing information materials, trainings and workshops for teachers, an internet page, newsletters, and financial support. In the school years 2007/08 and 2008/09, BEO'S was conducted at 14 primary and secondary schools in the district of Oberfranken, Bavaria. It was extended to other schools in 2009/10. The short- and mid-term goals are the improvement of the school's environments as well as the eating behaviour and physical activity of the students. In the long run, it is intended to prevent obesity and improve the students' health and school performance. The implementation processes showed that the teachers for physical education and domestic science as well as the headmasters were especially committed. The participation of the teaching staff, the students and the parents proved to be difficult, however. The schools implemented many activities for healthy eating and physical activity, but the planning process was not very systematic: needs assessment, status quo analysis, identification of successful strategies and definition of aims was difficult for the schools. The provided financial support, training programmes and workshops, and the exchange with other schools were widely used, in contrast to the offered internet-based tools. The acceptance of BEO'S was (very) good by teachers (n=97), students (n=674) and their parents (n=522). The teachers preferred the workshops and trainings to the internet page. The students appreciated the possibilities for physical activity and the emphasis on healthy eating; primary school students and girls more than secondary school students and boys. One third of the parents would like to be involved to a higher degree. BEO'S was well received by all the people involved. Yet, there are still deficits concerning the implementation process, especially in the participation of students and parents.