Objective The gut microbiota plays an important role in supporting overall health. Natural and safe substances that promote gut health and overall wellbeing are of great interest. This study examined the effect of Whole Cell Algae Fermentate (WCF) derived from Euglena gracilis on consistency and regularity of bowel habits and changes in fecal microbiome in healthy adults. Methods In this double-blind, randomized, placebo-controlled crossover study, 50 men and women (21-60 y, 18.5-43.9 kg/m2) with mild GI issues were supplemented with either placebo or 375 mg/d dried WCF for 4 weeks with a 3-week washout period. Before and after each 4-week intervention, subjects completed the Gastrointestinal Tolerance Questionnaire, Bowel Habits Diary, Perceived Stress Scale, and World Health Organization-Quality of Life Questionnaire. Circulating biomarkers, such as glucose, lipids, zonulin, and LPS-binding protein, were also assessed. Fecal microbiome was analyzed using a 16S rRNA amplicon sequencing method and fecal short-chain fatty acids (SCFA) were analyzed using a GC-MS method. Results The relative abundance of Bacteroidetes was larger with WCF intervention compared to placebo (p = 0.046) and the ratio of Firmicutes to Bacteroidetes (F/B) was smaller (p = 0.025). Shannon and Simpson α-diversity indices of fecal microbiome were significantly decreased by WCF compared to placebo (p <0.05). Bray-Curtis β-diversity index showed that WCF did not alter the overall fecal microbiome composition. There were no significant differences between placebo and WCF in GI symptoms, stool frequency and consistency, and ease of stool passage rating, perceived stress and quality of life scores, or fecal biomarkers. Significant within-group differences (p <0.05) were observed in the WCF group but not placebo for the gut permeability marker zonulin, ease of stool passage, fecal Actinobacteria, and the presence of five GI symptoms (gas/flatulence, abdominal cramping, abdominal distention/bloating, burping, reflux/heartburn). The result of a subgroup analysis of subjects with a decrease in the F/B ratio during the WCF intervention showed reduced Firmicutes (p <0.001) and Intestinibacter (p = 0.007)abundances in WCF compared to placebo. Additionally, the fecal branched SCFA, isovaleric (p = 0.038) and isobutryic acids (p = 0.042), were lower following WCF intervention compared to placebo. Conclusion Consumption of 375 mg/d dried WCF for 4 weeks improved F/B ratio, which has been linked with multiple beneficial health outcomes such as gut dysbiosis and metabolic syndrome. Interestingly, WCF decreased α-diversity of fecal microbiome, as has been observed with supplementation of prebiotic fibers. These microbial shifts were accompanied by potential objective improvements within the WCF group. Additionally, potentially harmful branched SCFA were reduced by WCF. This study is the first to show gut health improvements in humans following WCF supplementation.