Background <p>Probiotics may help bodybuilders by improving gut health, nutrient absorption, and reducing inflammation, potentially supporting muscle growth and fat loss. While research is promising, more studies are needed. This study explores the effects of probiotic supplementation on body composition and anthropometrics key measurements, aiming to see if they can support muscle building and fat management in unprofessional bodybuilders.</p> Methods <p>The research was conducted as a randomized, parallel, placebo-controlled clinical trial with a 12-week follow-up period. Participants were randomly assigned to one of the probiotic supplementations (<i>n</i> = 18), or placebo supplementation (<i>n</i> = 18). At the beginning and 12 weeks of the intervention, anthropometric indices and body composition were evaluated.</p> Results <p>A total of 80 participants (mean age, 29 years and mean weight, 74&#xa0;kg) were enrolled in this trial. After 12-week intervention, we observed WC, ABSI, BRI, BAI, AVI, and ConI significantly decreased in the probiotic group and BAI significantly decreased placebo group, with no significant differences observed between groups. Moreover, BMI, AVI, and ConI were significantly reduced in probiotic group in compare with the placebo group. No significant results were observed in other anthropometric and body composition indicators.</p> Conclusions <p>Probiotic supplementation improved anthropometric indices in unprofessional bodybuilders. However, these results need to be validated in a larger sample size.</p> Trial registration <p>Iranian Registry of Clinical Trials IRCT20240424061562N1, Registration date 20,240,730, Trial Id 77,722.</p>