Thistle () has been traditionally employed for liver protection. However, we recently identified silibinin, the main bioactive compound of thistle extract, as an in vitro pancreatic lipase inhibitor, which suggested a potential role as an anti-obesity agent. This study aimed to assess, in vivo, the efficacy, safety, and effects of silibinin on human lipase. As a secondary objective, we evaluated potential changes in gut microbiota after silibinin treatment. A randomized trial comparing 150 mg/silibinin, 300 mg/silibinin, and a thistle extract (equivalent to 150 mg/silibinin) with placebo and orlistat/120 mg was conducted. Fecal fat excretion, clinical parameters, and microbiota changes were analyzed. Orlistat showed the highest fecal fat excretion, although thistle extract had similar results ( = 0.582). The 150 mg/silibinin group reported the fewest adverse effects. Both silibinin and orlistat reduced plasma triglycerides ( = 0.016) and waist circumference ( = 0.001). Specific microbiota changes, such as increases in Mycobacteriaceae and Veillonellaceae, were associated with higher fat excretion. Although the present work was conducted in the short term and in people of normal weight, our results suggest that silibinin may be safe and effective for obesity, with minimal adverse effects and no significant changes in microbiota diversity. Further studies are needed to explore its microbiota-related benefits.