This dataset contains raw high-resolution mass spectrometry data from a randomized controlled trial evaluating probiotic supplementation in patients with metabolic dysfunction-associated steatotic liver disease (MASLD) (ClinicalTrials.gov Identifier: NCT04555434). Participants received placebo or probiotic capsules containing Pediococcus pentosaceus, Lactobacillus lactis, or Lactobacillus helveticus for 8 weeks. Fecal samples collected before and after intervention from participants with high medication adherence (at least 98%) were analyzed using untargeted metabolomic and lipidomic profiling. The data capture probiotic-associated alterations in fecal metabolites and lipid species related to gut-liver axis modulation and hepatic function.