Growing incidence of obesity and related diseases in children poses new challenges and calls for a review of lifestyle habits. This study aimed to assess daily eating habits (EH) and physical activity (PA) levels and identify their association with obesity in 8–10-year-old children. Children’s EH and time spent in moderate-to-vigorous physical intensity (MVPA) was estimated from questionnaires (N = 1788). Weight, height, and waist circumference (WC) were collected, and body mass index (BMI) calculated. Girls consumed more fruits and vegetables, drank more water, and ate smaller portions of carbohydrate and protein rich foods but spent less time in MVPA compared to boys (p < 0.05). Obese children skipped breakfast more often and consumed less fruits and vegetables. Children who chose to eat in front of the screen had higher WC (62.88 ± 8.70 vs 60.59 ± 7.40 cm, p < 0.001) and higher BMI, and chose smaller vegetable portions and more calorie dense snacks (p < 0.001). 15.4% of pupils covered weekly MVPA recommendations with structured PA on weekdays. Increasing MVPA was related to a smaller number of unhealthy EH (p < 0.001). In conclusion, EH and PA levels differ between sexes and obese children have unhealthier EH. Higher levels of MVPA are related to healthier food choices, while pupils having meals in front of the screen have unhealthier EH and anthropometric measures. The majority of pupils did not reach the WHO recommendations of MVPA through structured PA on weekdays. Association between factors (EH and time spent in PA) and BMI was not found in this study.