Introduction Over the last decades, dietary habits in developing countries have been characterized by low intake of fruits and vegetables and high consumption of sweetened drinks. Most of the evidence linking carbohydrate intake and asthma comes from children over 6 years of age. The aim of this study was to examine the association between macronutrient intake and the severity of asthma exacerbations in children aged 2–6 years. Methods We performed a cross-sectional study that included all children aged 2–6 years hospitalized due to an asthma exacerbation. Dietary data were collected using a food frequency questionnaire (FFQ) validated in the Colombian population. The GINA classification of acute asthma was used to define the severity. To identify factors independently associated with asthma exacerbation severity, we fit the data to ordinal logistic regression. Results During the study period, 228 cases of patients with asthma exacerbation were included. Asthma severity was dose-dependently associated with protein and carbohydrate-rich intake. The variables included in the multivariable analysis included reactive C protein (OR 1.05, CI 95% (1.03–1.07)), smoking at home (OR 3.92 (1.82–8.44)), atopic dermatitis (OR 3.82 (1.59–9.21)), and protein and carbohydrate-rich food intake (OR 0.11 (0.03–0.33)) and (OR 2.42 (1.09–5.80)), respectively. Conclusion High carbohydrate-rich food intake is associated with the severity of asthma exacerbation adjusted by other known risk factors such as atopy, smoking, and reactive C protein. This evidence should motivate the development of public health policies to control the consumption of sugar-rich products in children under 6 years.