Obesity is often associated with increased risk of cardiometabolic morbidities and mortality. However, evidence shows that some obese individuals are more likely to develop such risk factors early in life, including those with Metabolic Syndrome (MetS). Whether the presence of MetS in obese people impairs cardiac autonomic modulation (CAM) remains to be investigated. Cross-sectional study. Sixty-six subjects were classified as normal-weight (NW, n = 24) or obese (BMI ≥ 30 kg·m−2): metabolically healthy (MHO, n = 19) vs unhealthy (MUHO, n = 23: NCEP/ATPIII-MetS criteria). Body composition (bioimpedance), metabolic (glucose-insulin/lipid) and inflammatory profiles were determined. Linear and nonlinear heart rate variability (HRV) indices were computed at rest and during the submaximal six-minute step test (6MST). Blood pressure (BP) and metabolic and ventilatory variables were assessed (oxygen uptake, VO2; carbon dioxide production, VCO2; minute ventilation, VE) during the 6MST and the maximal cardiopulmonary exercise testing (CPX). All groups reached the same 6MST intensity (VO2 ~ 80% and HR ~ 87% of CPX peak values). Both obese groups, independently of MetS, presented higher BP and lower maximal VO2 than NW. However, HRV differed between groups according to MetS at rest and during exercise: MUHO had lower meanRRi and SD1 than NW and lower RMSSD and pNN50 than MHO at rest; during exercise, the lowest SDNN, TINN, SD1 and Shannon entropy were observed for MUHO. Significant correlations were found between MetS, insulin resistance and HRV indices; and between insulin resistance and aerobic capacity (VO2peak). Obesity per se impairs aerobic-hemodynamic responses to exercise. However, MetS in obese young adults negatively impacts overall HRV, parasympathetic activity and HRV complexity. •Cardiorespiratory responses to exercise are influenced by obesity per se.•Obese people with metabolic syndrome have impaired cardiac autonomic modulation.•The functional six-minute step test is useful to evaluate HRV.