The aims of the present study were to analyze the effects of 16 weeks of different aerobic exercise training (ExT) programs with diet on cardiac autonomic modulation and hemodynamics in nonphysically active and overweight/obese adults (n = 249, 53.7 ± 8.0 years) with primary hypertension, and the possible differences among ExT programs and their effects on heart rate (HR), blood pressure (BP), and long-term BP variability (BPV). Participants were randomly assigned into an attention control (AC) group (physical activity recommendations) or one of three supervised ExT groups: high volume of moderate-intensity continuous training, high-volume and high-intensity interval training (HIIT), and low-volume-HIIT. Twenty-four hours of ambulatory BP monitoring was used to analyze systolic (SBP) and diastolic (DBP) BP, HR, and BPV. A cardiopulmonary exercise test was performed to determine peak oxygen uptake (VO2peak). Following intervention, resting and submaximal exercise (HR, SBP, and DBP), along with diurnal and nocturnal SBP and DBP values decreased (P < 0.05) in all groups with no differences between groups. When the ExT groups were combined, submaximal SBP (P = 0.048) and DBP (P = 0.004), VO2peak (P = 0.014) and HR reserve (P = 0.030) were significantly improved compared with AC. Intervention did not have significant effects on BPV. In the present study better improvements in the autonomic nervous system were seen when the aerobic ExT was individually designed and supervised with pari passu effects irrespective of exercise intensity and volume. Low-volume-HIIT ExT combined with a healthy diet should be considered as a time efficient and safe mechanism for reducing the cardiovascular risk in hypertensive individuals.