(1) Background: Cardiopulmonary exercise testing (CPET) has been suggested by the European Society of Cardiology (ESC) for assessing the exercise limitations of apparently healthy individuals, but data on elite athletes regarding this test are scarce. (2) Methods: We analyzed CPET in elite (n = 43, 21.9 ± 3.7 years) and recreational (n= 40, 34.7 ± 13.0 years) athletes with persistent subjective exercise intolerance and post-exertional malaise (PEM) after COVID-19 infection. The primary outcome was the point prevalence of the adequate cardiopulmonary response (ACPR), defined by the presence of all of the following ESC criteria for apparently healthy individuals: (1) >100% of predicted peak oxygen consumption (predVO2peak), (2) VE/VCO2 < 30, (3) no exercise oscillatory ventilation (EOV), and (4) heart rate recovery of ≥12 beats/minute 1 min after exercise termination (HRR1). Results: ACPR occurred more frequently in elite athletes than in recreational athletes (70.0% vs. 39.5%;p= 0.005), mainly driven by the lower VE/VCO2 (<30: 97.7% vs. 65%,p< 0.001). Elite (11.6%) and recreational athletes (22.5%) showing a plateau of O2 pulse did not display ACPR. Conclusions: ACPR was not observed in all recreational and elite athletes with PEM. In particular, perturbed VE/VCO2 and the plateauing of O2 pulse are suitable for quantifying exercise limitations and may identify a high-risk population with long-COVID-19 syndrome who require their training intensities to be adapted.