Background and objectives: As a result of ergogenic properties, caffeine has been increasingly taken prior to physical exercise, yet its effects on post-exercise recovery, considering the differences in the cardiorespiratory capacity of the individuals, has not yet been studied or fully elucidated. Optimizing the post-exercise recovery can convey advantages to physical activity practitioners. We evaluated the acute effects of caffeine on heart rate (HR) autonomic control recovery following moderate aerobic exercise in males with different cardiorespiratory capacities. Materials and Methods: We split young adult men into two groups based on their various oxygen consumption peaks (VO(2) peak): (1) Higher VO(2) (HO): Sixteen volunteers, peak VO(2) > 42.46 mL/kg/min and (2) Low VO(2) (LO): Sixteen individuals, VO(2) < 42.46 mL/kg/min). The volunteers were submitted to placebo and caffeine protocols, which entailed 300 mg of caffeine or placebo (starch) in capsules, followed by 15 min of rest, 30 min of moderate exercise on a treadmill at 60% of the VO(2) peak, followed by 60 min of supine recovery. Heart rate variability (HRV) indexes in the time and frequency domains were examined. Results: Effect of time for RMSSD (square root of the average of the square of the differences between normal adjacent RR intervals) and SDNN (standard deviation of all normal RR intervals recorded in a time interval) was achieved (p < 0.001). Significant adjustments were observed (rest versus recovery) at the 0 to 5th min of recovery from exercise for the LO during the placebo protocol and at the 5th at 10th min of recovery for the caffeine protocol. For the HO in both procedures we found significant alterations only at the 0 to 5th min of recovery. Conclusion: Caffeine delayed parasympathetic recovery from exercise in individuals with lower cardiorespiratory capacity.