Dietary flavonoid intakes can influence gut microbiota (GM), which in turn can affect immune function and host metabolism, both vital considerations in cystic fibrosis (CF) management. In CF, GM may be altered and link to CF respiratory events. This study explored the relationship between flavonoid intakes and GM in free-living adults with CF. Associations between the overall GM variations (unweighted and weighted UniFrac distances between pyrosequencing results of bacterial 16-ss rDNA from frozen faecal samples of sixteen CF adults) and standardised dietary flavonoid intakes (a validated flavonoid-specific food frequency questionnaire) were analysed using adonis tests. Flavonoid intakes that were significant at a false discovery rate (FDR) < 0.3 were subjected to Spearman correlation tests with standardised bacterial relative abundances (FDR < 0.3). Gallocatechin intakes (p = 0.047, q = 0.285) were associated with unweighted UniFrac distances. Intakes of apigenin (p = 0.028, q = 0.227) and kaempferol (p = 0.029, q = 0.227), and % flavonoid intake as flavones (p = 0.013, q = 0.227) and flavonols (p = 0.016, q = 0.227) (both excluding contribution of tea) were associated with weighted UniFrac distances. Among these, gallocatechin correlated with the genus Actinomyces and family Actinomycetaceae (Actinobacteria). Gallocatechin correlated negatively with class Coriobacteriia (Actinobacteria). Intakes of some flavonoids may be associated with GM variations with potential consequences for metabolism, immune function, and inflammation, which are important in CF lung disease and co-morbidity management.