Background <p>Metabolic syndrome is a condition associated with mitochondrial dysfunction. Mitokines such as FGF-21 and GDF-15, recognized as biomarkers associated with metabolic stress, play crucial roles in regulating energy and inflammation. This study aimed to investigate the effects of High-Intensity Functional Training (HIFT) on the serum levels of FGF-21 and GDF-15, metabolic risk factors and body composition in middle-aged men with metabolic syndrome.</p> Methods <p>In a randomized controlled trial, 24 men (age = 42.40 ± 6.90 years) with metabolic syndrome were randomly assigned to either the HIFT group (<i>n</i> = 12) or the control group (<i>n</i> = 12). The HIFT group performed exercise sessions twice a week for 12 weeks, with each session lasting 50&#xa0;min. Anthropometric and biochemical assessments were conducted before and after the intervention.</p> Results <p>After the intervention, both primary outcomes—serum FGF-21 and GDF-15 levels—significantly decreased in the HIFT group (<i>P</i> = 0.001). Furthermore, body fat percentage, fasting blood glucose, HbA1c, blood lipids, and LDL-C decreased, whereas skeletal muscle mass and HDL increased (<i>P</i> &lt; 0.001).</p> Conclusion <p>Exercise training as HIFT was associated with improvements in select metabolic biomarkers by modulating the serum levels of mitokines, metabolic risk factors and body composition. These findings are associative and do not confirm direct mechanistic effects. Therefore, this type of training may be considered as a potential adjunctive non-pharmacological approach for the management of metabolic syndrome in middle-aged men, but further research with larger samples and active control groups is required.</p> Trial registration <p>Iranian Registry of Clinical Trials identifier: IRCT20241130063899N1, prospectively registered 01-11- 2025, <a href="https://irct.behdasht.gov.ir/trial/80642">https://irct.behdasht.gov.ir/trial/80642</a>.</p>