Background: The COcoa Supplement and Multivitamin Outcomes Study (COSMOS) is a recently completed randomized, double-blind, placebo-controlled, 2x2 factorial trial of a multivitamin and cocoa extract supplement (containing 500 mg/d flavanols) in 21,442 older adults. In view of favorable effects of multivitamins on cognition and promising signals for cardiovascular risk reduction with cocoa extract, we conducted a pilot study to explore whether these interventions affected gut microbial composition and function. Methods: We conducted deep shotgun metagenomic sequencing in 30 COSMOS participants using fecal samples collected at baseline and year 2. We performed taxonomic profiling using MetaPhlAn2 and functional profiling using HUMAnN2. After proper quality filtering, we analyzed effects of both interventions on 2-year changes in microbial features, adjusting for age, sex, and body mass index. Results: Cocoa extract supplementation significantly altered the overall gut microbial taxonomic compositions from baseline to year 2, and explained 5.5% of the variance in the 2-year changes in relative abundance of all microbial species ( P =0.008). We further found that randomized cocoa extract supplementation altered the relative abundance of a few microbial species, including those previously linked to anti-inflammatory and cardiometabolic benefits (e.g., Akkermansia muciniphila , nominal P <0.05), and several microbial super pathways (including pyrimidine ribonucleotides de novo biosynthesis, FDR=0.03, and 28 other pathways with nominal P <0.05). Randomized multivitamin use did not significantly affect 2-year changes in alpha or beta diversity, but altered the abundance a few putative bacterial species and functional pathways (nominal P <0.05). Summary: Our pilot study suggests that cocoa extract and multivitamin supplementation in COSMOS may alter the gut microbiome and influence pathways relevant to health, emphasizing the need for larger studies that allow for more detailed investigations.