Abstract Exhaled breath condensate (EBC) analysis is a recently developed, non-invasive method used to identify and quantify biomarkers, mainly those coming from the lower respiratory tract. It seems that diet can influence the airway’s inflammation and change the exhaled breath composition. This study aimed to assess the association between diet quality intake and markers in EBC among school-aged children. A cross-sectional analysis included 150 children (48.3% females, aged 7–12 years, mean age: 8.7 ± 0.8 years) from 20 schools across Porto, Portugal. We assessed diet quality through the Healthy Eating Index (HEI)-2015, which was estimated based on a single 24 h food recall questionnaire. EBC samples were collected, and we assessed their ionic content (Na+, K+) and conductivity. The association between diet quality and Na+, K+, Na+/K+ ratio and conductivity was estimated using logistic regression models adjusted for potential confounders. After adjustment, a higher quality diet score increases the odds of higher conductivity values of the EBC (aOR = 1.04, 95%CI 1.00; 1.08). Our findings suggest that a higher diet quality in school-aged children is associated with higher conductivity levels of the EBC.