Background: The cardiovascular effects of SARS-CoV-2 in elite athletes are still a matter of debate. Accordingly, we sought to perform a comprehensive echocardiographic characterization of post-COVID athletes by comparing them to a non-COVID athlete cohort.Methods: 107 elite athletes with COVID-19 were prospectively enrolled (P-CA; 23 ± 6 years, 23% female) 107 healthy athletes were selected as a control group using propensity score matching (N-CA). All athletes underwent 2D and 3D echocardiography. Left (LV) and right ventricular (RV) end-diastolic volumes (EDVi) and ejection fractions (EF) were quantified. To characterize LV longitudinal deformation, 2D global longitudinal strain (GLS) and the ratio of free wall vs. septal longitudinal strain (FWLS/SLS) were also measured. To describe septal flattening (SF—frequently seen in P-CA), LV eccentricity index (EI) was calculated.Results: P-CA and N-CA athletes had comparable LV and RVEDVi (P-CA vs. N-CA; 77 ± 12 vs. 78 ± 13mL/m2; 79 ± 16 vs. 80 ± 14mL/m2). P-CA had significantly higher LVEF (58 ± 4 vs. 56 ± 4%, p < 0.001), while LVGLS values did not differ between P-CA and N-CA (−19.0 ± 1.9 vs. −18.8 ± 2.2%). EI was significantly higher in P-CA (1.13 ± 0.16 vs. 1.01 ± 0.05, p < 0.001), which was attributable to a distinct subgroup of P-CA with a prominent SF (n = 35, 33%), further provoked by inspiration. In this subgroup, the EI was markedly higher compared to the rest of the P-CA (1.29 ± 0.15 vs. 1.04 ± 0.08, p < 0.001), LVEDVi was also significantly higher (80 ± 14 vs. 75 ± 11 mL/m2, p < 0.001), while RVEDVi did not differ (82 ± 16 vs. 78 ± 15mL/m2). Moreover, the FWLS/SLS ratio was significantly lower in the SF subgroup (91.7 ± 8.6 vs. 97.3 ± 8.2, p < 0.01). P-CA with SF experienced symptoms less frequently (1.4 ± 1.3 vs. 2.1 ± 1.5 symptom during the infection, p = 0.01).Conclusions: Elite athletes following COVID-19 showed distinct morphological and functional cardiac changes compared to a propensity score-matched control athlete group. These results are mainly driven by a subgroup, which presented with some echocardiographic features characteristic of constrictive pericarditis.