We assessed, for the first time, to what extent the composition of the gut microbiome might explain the cross-sectional association of habitual flavonoid and flavonoid-rich food intake with systolic and diastolic blood pressure (BP) in a community-based sample (N=904) from Northern Germany. Gut microbiome composition was sequenced from 16S ribosomal RNA genes. Higher total flavonoid intakes and specifically the polymer subclass were associated with lower systolic BP (SBP; β T3-T1: −2.9% [95% CI, −5.1 to −0.7], P =0.01 and −3.7% [95% CI, −5.4 to −1.0], P =0.01). In food-based analyses, a higher intake of berries (SBP, β Q4-Q1: −2.9% [95% CI, −5.2 to −0.6], P =0.01; pulse pressure, −5.5% [95% CI, −9.6 to −1.2], P =0.01) and red wine (SBP, β Q4-Q1: −2.6% [95% CI, −4.8 to −0.3], P =0.03; pulse pressure, −6.1% [95% CI, −10.1 to −2.0], P <0.01) were associated with lower SBP and pulse pressure. There were no associations with diastolic BP. In food-based analyses, higher intakes of anthocyanin-rich berries and red wine were associated with higher alpha diversity (β Q4-Q1: 0.03 [95% CI, 0.0–0.1], P =0.04 and 0.1 [95% CI, 0.03–0.1], P <0.01). Higher intakes of berries and apples/pears were associated with a lower abundance of Parabacteroides (β Q4-Q1: −0.2 [95% CI, −0.4 to −0.1], P <0.01, Q=0.07 and −0.3 [95% CI, −0.4 to −0.1], P < 0.01, Q =0.04). Structural equation modeling of these novel data suggests that microbial factors explained 15.2% to the association between flavonoid-rich foods and clinically relevant lower SBP. Further research should focus on interindividual variability in the gut microbiome in mediating the cardiovascular effects of flavonoid-rich foods.