Abstract Background We aimed to compare the effects of 3 different upright seated recovery protocols on heart rate recovery (HRR) after a submaximal ergometer exercise. Methods The study included 30 young adult volunteers (15 men and 15 women). Participants performed a submaximal cycle exercise test at a constant workload of 60 Watts until a steady HR was achieved. This was followed by 5 min of: (a) inactive, (b) active loadless, and (c) passive recovery protocols. The HRR was assessed as the difference between the peak exercise HR and the HR recorded following 1 min of recovery and as the percentage HR decline after 1 min postexercise. Abnormal HRR was defined as a reduction of 1-min HRR ≤12 b · min−1 or ≤15 b · min−1 or ≤18 b · min−1. Results In both sexes, HRR was faster during inactive recovery compared with active recovery. In males, HRR was faster during inactive recovery compared with passive recovery protocol. In females, HRR was faster during passive recovery compared with active recovery protocol. The prevalence of impaired HRR was greater in the active recovery compared with the passive and inactive recovery protocols in both sexes. Conclusion The present findings suggest that in both sexes, the postexercise HRR was mediated by a combined action of the central command and other inputs or stimuli arising from skeletal muscle activities. In addition, the active recovery protocol resulted to a slower HRR and elicited more abnormal postexercise HR responses compared with the other recovery protocols.