ObjectivesTo analyze the evolution of clinical and anthropometric characteristics of children and adolescents with cystic fibrosis (CF) over 24 months, including the period of the COVID‐19 pandemic.MethodsA longitudinal study with data collection from May 2018 to November 2020 in physical and electronic records from a pediatric reference center, including individuals with CF aged up to 18 years.ResultsThe sample encompassed 72 individuals. Weight (p < 0.01), height (p < 0.01), and body mass index (BMI) (p = 0.043) were higher in 2020 than in 2018. There were no significant changes in BMI‐Z (p = 0.977) and in percentiles of weight (p = 0.540), height (p = 0.458), and BMI percentile (p = 0.454) between both periods. Pancreatic insufficiency was observed in 91.7% of patients in 2020, and there were twice as many confirmed cases of diabetes compared to 2018. There was a 9.7% increase in individuals colonized by the oxacillin‐sensitive Staphylococcus aureus (OSSA) (p = 0.039) and an 11.1% reduction in non‐colonized individuals (p = 0.008).ConclusionAlthough there was an increase in weight, height, and BMI from 2018 to 2020, there were no significant changes in BMI‐Z and in percentiles of weight, height, and BMI percentile, suggesting that the anthropometric aspects of nutritional status did not change in this period of 2 years. Moreover, there was an increase in the prevalence of individuals colonized by OSSA and a reduction in the prevalence of individuals non‐colonized with any bacteria.