Interventions via the Internet are promising regarding the promotion of healthy habits among youth. The objective of this study was to evaluate the effect of an adapted version of StayingFit to promote healthy eating habits and the measurement adequacy of anthropometric markers among adolescents. A web school-based 12-month cluster-randomized controlled trial examining 7th to 9th grade students was conducted in twelve schools in Salvador, Bahia, Brazil. The schools’ students were randomly distributed into the intervention and control groups. The intervention group participated in StayingFit, an online program designed to encourage and guide healthy eating habits and control body weight. Data on food consumption, anthropometry, physical activity level, and sedentary behavior were collected from all of the students at the beginning of and after the 12-month study. Demographic and socioeconomic data were collected at baseline. The baseline data indicated high rates of overweight (14.4% overweight and 8.5% obese), insufficiently active (87.6%), and sedentary (63.7%). Furthermore, few adolescents regularly consumed fruits (18.8%) and vegetables/legumes (16.4%). Generalized estimating equations (GEEs) were used to evaluate the effect of the intervention. At the end of the follow-up period, students in the intervention group had a 43% increased chance of regularly consuming beans (OR = 1.43, 95% CIs = 1.10–1.86) and a 35% decreased chance of regularly consuming soft drinks (OR = 0.65, 95% CIs = 0.50–0.84). No differences were found between the groups studied with regard to the anthropometric parameters. Despite these modest results, the implementation of a web intervention can be beneficial and help promote positive changes in adolescent eating habits.