Ecuador is undergoing a nutrition transition where overweight/obesity coexist with undernutrition. The objective of this study was to determine nutritional status, physical activity, fruit and vegetables consumption frequency among school-going adolescents in the canton of Paute and further explore if these variables were differential by urban vs. rural residence. We conducted a cross-sectional study using a random sample of students aged 12 to 19 years from the only two public secondary schools in the canton Paute. We determined nutritional status according to the World Health Organization criteria. Demographics, physical activity habits, fruit and vegetable consumption frequency were determined by questionnaires. Of the total of 314 students, 44.9% lived in urban area and 55.1% in rural area. The prevalence of overweight/obesity was significantly higher among students with urban vs. rural residence (28.4% vs. 17.9%; P=.03). The prevalence of stunting was significantly higher among students with rural vs. urban residence (31.8% vs. 16.3%; P=.002). There were no significant differences detected between groups in the frequency of consumption of fruits and vegetables. Urban residence was associated with a greater mean number of minutes of outdoor recreation after school (76.0 minutes vs. 57.1 minutes; P=.02), greater weekly hours of planned physical activity (2.0 hours vs. 1.6 hours; P=.007), and greater daily screen time in front of a television or computer (3.2 hours vs. 2.5 hours; P<.001). Interventions to prevent or reduce overweight/obesity in Paute and other similar areas with students from both urban and rural areas should consider place of residence in their design(AU)