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Background Dietary supplements that combine vitamins, minerals, phytonutrients, prebiotics, and probiotics have gained popularity among health-oriented consumers seeking convenient ways to fill nutritional gaps and support gut health. Methods This randomized, double-blind, placebo-controlled crossover study examined the effects of two weeks of the nutritional supplement (AG1 ® ) on gut microbial composition, nutritional adequacy, and tolerability. Twenty resistance-trained men ( n = 10; 26.4 ± 6.5 y) and women ( n = 10; 26.9 ± 5.3 y) supplemented daily with either AG1 ® or placebo (PL) for 14 days. Following a 2-week washout, participants crossed over to the other condition. Participants provided stool samples for gut microbial composition analysis, completed the Digestion-associated Quality of Life Questionnaire (DQLQ), and completed a 24-h dietary intake assessment at the beginning and end of each 14-day supplementation period. Outcomes were analyzed using repeated-measures and multivariate statistical approaches for dietary intake, gut microbiota, metabolomics, and questionnaire data. Results AG1 ® did not produce large, global shifts in microbial alpha or beta diversity, supplementation was associated with selective enrichment of key bacterial taxa commonly linked to gut health, including Lactiplantibacillus plantarum, Lacticaseibacillus rhamnosus , and Bifidobacterium animalis . AG1 ® supplementation significantly improved nutritional adequacy by increasing the total number of micronutrient Estimated Average Requirements (EARs) met compared to placebo (2.8; p = 0.0011), with no significant differences in digestive quality of life between groups ( p = 0.777). Vitamins A, C, and E were the most common nutrient gaps filled by AG1 supplementation. Conclusions Two weeks of AG1 ® supplementation improved micronutrient adequacy in healthy resistance-trained adults by reducing nutrient gaps. Supplementation also selectively enriched key beneficial gut microbial taxa and putative microbial functional without inducing major disruptions to overall community structure. Importantly, AG1 ® was well tolerated and did not negatively impact digestion-associated quality of life. Clinical trial registration ClinicalTrials.gov , identifier: NCT06521424.