Infants and children are a risk group in terms of developing healthy habits, an important aspect if we consider that many of them were born during the COVID-19 pandemic. Our objective was to evaluate compliance with lifestyle recommendations proposed at the national and international levels in children aged 0 to 23 months during confinement due to the COVID-19 pandemic in Chile. A cross-sectional study was conducted, and 211 online questionnaires were completed with sociodemographic and lifestyle information of children. Our results show high compliance with the recommendations on breastfeeding intake (78.3% and 69.5% in 0–5-month-old and 6–23-month-old children, respectively); age of starting complementary feeding (87.4%); non-consumption of salt and sugar (80.1%), non-caloric sweeteners (90.7%), and sweet and salty snacks (68.9%); and hours of physical activity (66.8%) and sleep (65.4%). However, we observed low compliance with the recommendations on the age of introduction of dinner (58.0%), eggs (23.0%), legumes (39.2%), and fish (35.1%); low consumption of legumes (43.4%) and fish (20.5%); and low compliance with the recommendations on screen use during meals (59.2%) and daily screen hours (41.2%). In conclusion, feeding behavior, physical activity, use of screens, and hours of sleep in children were altered by confinement during the pandemic, harming the development of healthy lifestyles.