Sub-optimal feeding practices among under-5 children are the major drivers of malnutrition. This study aims to assess the prevalence of malnutrition and the factors affecting exclusive breastfeeding, bottle feeding, and complementary feeding practices among under 5 children amid the COVID-19 pandemic as well as the economic and the political crises in Lebanon. A nationally representative stratified random sample of mother–child dyads (n = 511) was collected from households using a stratified cluster sampling design. The survey inquired about infant’s feeding and complementary feeding practices using a valid questionnaire. Anthropometric measurements of the mother and child were collected. Multivariate logistic regression was conducted to explore the determinants associated with under-5 children’s practices. The prevalence of underweight, stunting, wasting, overweight and obese children was 0.5%, 8.4%, 6.7%, 16.8% and 8.9%, respectively. In total, among under-5 children, the prevalence of ever breastfeeding, exclusive breastfeeding, and bottle feeding at birth was 95.1%, 59.1% and 25.8%, respectively. Half the children in this study started solid foods between 4 and 6 months. Regression analysis showed that supporting breastfeeding at hospital (aOR = 8.20, 95% CI (3.03–22.17)) and husband’s support (aOR = 3.07, 95% CI (1.9–4.92)) were associated with increased breastfeeding odds. However, mother’s occupation (aOR = 0.18, 95% CI (0.55–0.58)) was inversely associated with breastfeeding practices. Male children (aOR = 2.119, 95% CI (1.37–3.27), mothers diagnosed with COVID-19 (aOR = 0.58, 95% CI (0.35–0.95)), and bottle feeding at hospital (aOR = 0.5, 95% CI (0.32–0.77)) were more likely to induce early initiation of solid foods at 4 months of age. This study demonstrated non-negligible rates of malnutrition, low prevalence of exclusive breastfeeding, and high rates of early introduction of formula feeding and solid foods among Lebanese under-5-children amid escalating crises.