The development of healthy eating habits in adolescence is perceived as an effective strategy to avoid health problems in adulthood. The involvement of educational centres’ governing boards, as well as the Educational State and Regional Administrations’, may be necessary to create healthy food environments during the school day. The objective of this study is to identify the relationship between students’ eating habits during the school day and sociodemographic, family and physical activity variables, as well as the existence of a school cafeteria. For this, a cross-sectional study in a stratified random sample of 8068 students of Public Secondary Education High Schools of Andalusia (Spain) has been carried out. The results show that students who are 14 years old or older are more likely to skip breakfast at home (odds ratio (OR): 1.81, 95% confidence interval (CI): 1.55–2.12) than those under this age. Students whose mothers do not have a university education are more likely to consume incomplete breakfasts (OR: 1.83, 95% CI: 1.26–2.65). Snacks with sweets (OR: 1.93, 95% CI: 1.67–2.23), candy in general (OR: 2.75, 95% CI: 2.38–3.19), and bagged crisps (OR: 3.06, 95% CI: 2.65–3.54) were more likely to be consumed in schools with a cafeteria. The factors that significantly influence the eating habits of secondary students in Andalusia include age, sex, parental level of education, physical activity and the existence of a cafeteria.