Introduction: Altered gut and vaginal microbial communities are linked to adverse pregnancy outcomes. Diet is a major modifiable factor shaping the microbiome. This study examined associations between dietary scores and gut and vaginal microbiome profiles in early pregnancy. Methodology: Healthy pregnant women (n=130) were analysed from the MicrobeMom trial. In early pregnancy, women completed food frequency questionnaires used to calculate Alternate Healthy Eating Index for Pregnancy (AHEIP), Mediterranean Diet (MD), Planetary Health Diet Index (PHDI), Dietary Approaches to Stop Hypertension (DASH), and Dietary Inflammatory Index (DII) scores. Stool samples and vaginal swabs were obtained. Microbiome composition was assessed using shotgun metagenomic sequencing and alpha and beta diversity calculated. Community state type (CST) was assigned to all vaginal samples. Relationships between diet scores and microbial diversity were explored continuously and between ‘high’ and ‘low’ scoring groups based on the median of each diet score. Results: Higher DII scores, reflecting more pro-inflammatory diets, were associated with reduced stool Shannon diversity (p=0.033;τ=-0.132) and Simpson diversity (p=0.011;τ=-0.157). Higher AHEIP scores were associated with increased Simpson diversity (p=0.03;τ=-0.129). Beta diversity analysis revealed differences in vaginal microbiome composition between the ‘High’ and ‘Low’ AHEIP groups (p=0.022;R2=0.02). Similar group differences were observed in stool microbiome composition for AHEIP (p=0.004;R2=0.018) and DASH (p=0.014;R2=0.015) scores. Women with lower AHEI-P and DASH scores had significantly higher relative abundance of Lactobacillus iners in the vaginal microbiome (AHEI-P: Wilcoxon p=0.00088; DASH: Wilcoxon p=0.02). Conclusion: Dietary quality was associated with distinct differences in gut and vaginal microbial diversity and composition in early pregnancy.