Background <p>Metabolic syndrome (MetS) represents a well-recognized contributor to cardiovascular risk, and synbiotics have recently gained attention as a potential dietary strategy for its management. The present study aimed to determine whether a novel synbiotic yogurt formulated with <i>Lactobacillus plantarum</i>,<i> Lactobacillus pentosus</i>, and the yeast <i>Kluyveromyces marxianus</i> affects atherogenic markers, cardiometabolic parameters, and insulin resistance surrogates in individuals among individuals diagnosed with MetS.</p> Methods <p>A 12-week double-blind, standard-yogurt-controlled randomized clinical trial was conducted, enrolling 44 adults with MetS who were randomized to either 300&#xa0;g/day of synbiotic yogurt (<i>n</i> = 22) or a matched control yogurt (<i>n</i> = 22); 41 (22 synbiotic, 19 control yogurt) completed and were analyzed. A comprehensive panel of cardiometabolic outcomes was evaluated at baseline and week 12, encompassing atherogenic indices including the Atherogenic Index of Plasma (AIP), Castelli’s Risk Index-I (CRI-I), Castelli’s Risk Index-II (CRI-II), Atherogenic Coefficient (AC), and oxidized low-density lipoprotein (ox-LDL); cardiometabolic measures including the Visceral Adiposity Index (VAI), Waist Triglyceride Index (WTI), and Cardiometabolic Index (CMI); body shape and adiposity indices including A Body Shape Index (ABSI), Body Roundness Index (BRI), Body Adiposity Index (BAI), Conicity Index, Abdominal Volume Index (AVI), and Weight-adjusted Waist Index (WWI); and surrogate markers of insulin resistance including the Triglyceride-Glucose Index (TyG), Hepatic Steatosis Index (HSI), triglyceride to high-density lipoprotein ratio (TG/HDL), TyG-Body Mass Index (TyG-BMI), TyG-Waist Circumference (TyG-WC), Metabolic Score for Insulin Resistance (METS-IR), and Lipid Accumulation Product (LAP).</p> Results <p>At the end of the 12-week period, statistically significant between-group differences were limited to four indices, namely CRI-I (<i>p</i> = 0.039), CRI-II (<i>p</i> = 0.038), AC (<i>p</i> = 0.039), and BAI (<i>p</i> = 0.027), all of which favored the control group. Within-group analyses indicated that the control arm experienced significant reductions in AIP, CRI-I, CRI-II, AC, TG/HDL, and METS-IR, whereas participants in the synbiotic arm demonstrated significant decreases only in TyG and TyG-BMI. No significant changes were observed in other indices.</p> Conclusions <p>According to our findings, 12 weeks of daily synbiotic yogurt consumption did not significantly improve insulin resistance surrogates, atherogenic, and novel anthropometric indices in adults with MetS.</p> Trial registration number <p>Iranian Registry of Clinical Trials (registration ID: IRCT20220426054667N1; registration date: 2022-05-18).</p>