Background: Flavonoid intake modifies the composition of the gut microbiome, which contributes to the metabolism of flavonoids. Few studies have examined the contribution of the gut microbiome to the health benefits associated with flavonoid intake. Objectives: We aimed to examine associations between habitual intakes of flavonoid subclasses and MRI-determined visceral (VAT) and subcutaneous (SAT) adipose tissue. Uniquely, we also identified associations between the aforementioned measurements and gut microbiome composition sequenced from 16S ribosomal RNA genes. Methods: We undertook cross-sectional analyses of 618 men and women (n = 368 male), aged 25-83 y, from the PopGen cohort. Results: Higher intake of anthocyanins was associated with lower amounts of VAT [tertile (T)3-T1:-0.49 dm³; β:-8.9%; 95% CI:-16.2%,-1.1%; P = 0.03] and VAT:SAT ratio (T3-T1:-0.04; β:-7.1%; 95% CI:-13.5%,-0.3%; P = 0.03). Higher intakes of anthocyanin-rich foods were also inversely associated with VAT [quantile (Q)4-Q1:-0.39 dm³; β:-9.9%; 95% CI:-17.4%,-1.6%; P = 0.02] and VAT:SAT ratio (Q4-Q1:-0.04; β:-6.5%; 95% CI:-13.3%,-0.9%; P = 0.03). Participants with the highest intakes of anthocyanin-rich foods also had higher microbial diversity (Q4-Q1: β: 0.18; 95% CI: 0.06, 0.31; P < 0.01), higher abundances of Clostridiales (Q4-Q1: β: 449; 95% CI: 96.3, 801; P = 0.04) and Ruminococcaceae (Q4-Q1: β: 313; 95% CI: 33.6, 591; P = 0.04), and lower abundance of Clostridium XIVa (Q4-Q1: β:-41.1; 95% CI:-72.4,-9.8; P = 0.04). Participants with the highest microbial diversity, abundances of Clostridiales and Ruminococcaceae, and lower abundance of Clostridium XIVa had lower amounts of VAT. Up to 18.5% of the association between intake of anthocyanin-rich foods and VAT could be explained by the gut microbiome. Conclusions: These novel data suggest that higher microbial diversity and abundance of specific taxa in the Clostridiales order may contribute to the association between higher intake of anthocyanins and lower abdominal adipose tissue.