A significant decline in pulmonary exacerbation rates has been reported in CF patients homozygous for F508del treated with lumacaftor/ivacaftor. However, it is still unclear whether this reduction reflects a diminished microbiological burden. The aim of this study was to determine the impact of lumacaftor/ivacaftor on the bacterial and fungal burden. The study is a prospective multicenter cohort study including 132 CF patients homozygous for F508del treated with lumacaftor/ivacaftor. Clinical parameters as well as bacterial and fungal outcomes 1 year after initiation of lumacaftor/ivacaftor were compared to data from 2 years prior to initiation of the treatment. Changes in the slope of the outcomes before and after the onset of treatment were assessed. Lung function measured as ppFEV1 (  < 0.001), body mass index (BMI) in adults (  < 0.001), and BMI -score in children (  = 0.007) were improved after initiation of lumacaftor/ivacaftor. In addition, the slope of the prevalence of (  = 0.007) and (  < 0.001) shifted from positive to negative, that is, became less prevalent, 1 year after treatment, while the slope for (  = 0.009), spp (  = 0.026), and (  < 0.001) shifted from negative to positive. The current study showed a significant improvement in clinical parameters and a reduction of some of CF respiratory microorganisms 1 year after starting with lumacaftor/ivacaftor. However, no significant changes were observed for , or , key pathogens in the CF context.