Aim: The primary aim of this clinical study was to determine if dietary supplementation with the probiotic, BIOHM FX (BFX), altered the gut microbiome balance following ingestion of 15g pea protein (PP) and enhanced the absorption of non-animal proteins determined via quantification of essential amino acids (EAAs). Thus, we compared the effects of pea protein alone vs. pea protein + BFX on microbiome changes and plasma levels of EAAs. Methods: A placebo-controlled crossover clinical study in active men (n=40) was performed during which quantification of abundance levels of gut bacterial and fungal (bacteriome and mycobiome) organisms were assessed. In addition, plasma EAAs were measured pre- and post- ingestion of the pea protein +/-BFX for 180 min. Stool samples were analyzed for changes in microbiome composition from baseline and compared for PP versus PP+BFX. Self-reported changes in gastrointestinal (e.g., bloating, flatulence) and quality of life (e.g., fatigue, mood, and energy) indices were also measured. Results: Participants ingesting PP + BFX exhibited a distinct microbiome profile compared to baseline and ingestion of PP. Differences in plasma EAAs showed a trend for an interaction (P=0.097) and post hoc testing at 120 min showed a significant difference (P=0.047) between PP and PP+BFX. Microbiome analysis of stool samples showed that the pathogens Escherichia coli, Prevotella copri, Shigella flexneri, and Brevundimonas diminuta were lower in PP+BFX compared to PP. The abundance of Candida albicans was lower and the level of Saccharomyces cerevisiae was higher in PP+BFX compared to PP. Interestingly, the abundance of Pseudomonas species, cyanobacteria phyla and the fungal species Galactomyces geotrichum were elevated when the combination of PP+BFX were consumed by study subjects (P<0.05). Other than main effects of time there were no significant differences between treatments in self-reported gastrointestinal (GI) and well-being markers. Conclusion: Our results indicate that the addition of BFX to PP alters the gut microbiome composition, aiding in the absorption of dietary non-animal proteins and increasing essential amino acid appearance in plasma.