Abstract Background and Aim Both interval ( IT ) and continuous ( CT ) exercise training results in an improvement of aerobic capacity in patients with chronic obstructive pulmonary disease ( COPD ); however, their effects on cardiac autonomic function remains unclear. The aim of our study was to evaluate the effect of a supervised CT vs IT on autonomic cardiac function in COPD patients. Methods COPD patients were divided into two different groups according to training modality ( IT or CT ). Autonomic cardiac dysfunction ( ACD ) was defined as a heart rate recovery lower than 12 bpm heart rate after the first minute of maximal exercise ( HRR 1 ) and an abnormal chronotropic response ( CR ) to exercise (<80%). Results A total of 29 patients {mean [standard deviation ( SD )] age: 68 (8) years, % FEV 1 : 42 (13) predicted} were trained (15 subjects in the CT group, 14 subjects in the IT group). After training, both groups increased peak oxygen consumption [mean difference Δ VO 2 peak: 156 mL/min ( P = 0.04) on IT ; and 210 mL/min ( P = 0.01) on CT ], HRR 1 [ IT , from 10.4 (5) to 13.8 (5) bpm ( P = 0.04); and CT , from 14.3 (5) to 17.7 (5) bpm ( P = 0.04)] and CR [ IT , from 57% (22) to 81% (9) ( P = 0.001); and CT , from 48% (28) to 73% (17) ( P = 0.001)]. Sixteen patients showed ACD . Among these patients, HRR 1 ( P = 0.01 for IT and P = 0.04 for CT ) and CR ( P = 0.001 for IT and P = 0.002 for CT ) were enhanced after training. Conclusions Both IT and CT exercise training improve heart rate recovery and CR in COPD patients. These benefits could help to individualize exercise training.