Purpose <p>Our aim was to examine the effects of combined prebiotic fiber supplementation and weight loss counseling on liver fat, body composition, subjective appetite, serum metabolomics, and intestinal microbiota in adults with MASLD.</p> Methods <p>In a double blind, placebo-controlled trial, adult participants aged 18–70&#xa0;years old with MASLD were randomized to receive prebiotic (oligofructose-enriched inulin, 16&#xa0;g/day; n = 22) or isocaloric placebo (maltodextrin; n = 20) for 24&#xa0;weeks alongside weight loss counseling from a registered dietitian. Primary outcomes were change in intrahepatic fat % (IHF%) and hepatic injury from baseline to 24&#xa0;weeks. Secondary outcomes included body composition, subjective appetite, serum lipids and cytokines, fecal microbiota, and serum metabolomics.</p> Results <p>At baseline, participants had IHF of 14.4 ± 8.4%. The change in IHF from baseline to 24&#xa0;weeks did not differ between prebiotic and placebo. Prebiotic participants had a greater decrease (<i>p</i> = 0.029) in percent trunk fat compared to placebo. Compared to placebo, prebiotic significantly decreased desire to eat and hunger ratings over the course of the intervention. Fecal microbiota analysis showed a significant increase in <i>Bifidobacterium</i> abundance with prebiotic. A pathway analysis based on untargeted serum metabolomics revealed a downregulation of taurine and hypotaurine metabolism in the placebo group which was conserved in the prebiotic group.</p> Conclusion <p>Adding prebiotic fiber supplementation to weight loss counseling for adults with MASLD enhanced reductions in trunk fat and had a beneficial effect on subjective appetite compared to placebo. Improvements in fecal microbial profile and taurine metabolism revealed specific beneficial effects of prebiotics in the management of MASLD.</p> Clinical Trial Registration <p>Clinicaltrials.gov/study/NCT02568605.</p>