Lockdown during the COVID-19 pandemic imposed changes in children’s daily routine that could lead to changes in behavior patterns. Using a survey targeted at children under 17 years of age, we described dietary (adherence to Mediterranean diet, AMD) and sleeping habits (disorders of initiating and maintaining sleep) after the implementation of lockdown, and examined the probability of the inadequate frequency of physical activity (PA) and use of TV and electronic devices (TV-ED) before and after lockdown through generalized estimating equation models, accounting for age and gender differences. From 3464 children included, 53.2% showed optimal AMD; 79.2% referred to delayed bedtime; and 16.3% were suspected of sleeping disorders after the implementation of lockdown. Delay in bedtime was more frequent among children older than 6 years, and inadequate sleeping hours among those younger than 11 years. There were no gender differences in AMD or sleeping habits. The odds of inadequate frequency of PA and TV-ED use were greater after lockdown, with a greater risk for TV-ED use. Boys were at greater risk of inadequate PA frequency and TV-ED use. Odds ratio of inadequate PA was greater at older ages. Lockdown could influence changes in children’s habits that could lead to risk factors for non-communicable diseases during adulthood if such behaviors are sustained over time.