Plant-based diets are a growing trend, including among athletes. This study compares the differences in physical performance and heart morphology and function between vegan and omnivorous amateur runners. A study group and a matched control group were recruited comprising N = 30 participants each. Eight members of the study group were excluded, leaving N = 22 participants. Members of both groups were of similar age and trained with similar frequency and intensity. Vegans displayed a higher VO2max (54.08 vs. 50.10 mL/kg/min, p < 0.05), which correlated positively with carbohydrate intake (ρ = 0.52) and negatively with MUFA (monounsaturated fatty acids) intake (ρ = −0.43). The vegans presented a more eccentric form of remodelling with greater left ventricular end diastolic diameter (LVEDd, 2.93 vs. 2.81 cm/m2, p = 0.04) and a lower relative wall thickness (RWT, 0.39 vs. 0.42, p = 0.04) and left ventricular mass (LVM, 190 vs. 210 g, p = 0.01). The left ventricular mass index (LVMI) was similar (108 vs. 115 g/m2, p = NS). Longitudinal strain was higher in the vegan group (−20.5 vs. −19.6%, p = 0.04), suggesting better systolic function. Higher E-wave velocities (87 vs. 78 cm/s, p = 0.001) and E/e′ ratios (6.32 vs. 5.6, p = 0.03) may suggest better diastolic function in the vegan group. The results demonstrate that following a plant-based diet does not impair amateur athletes’ performance and influences both morphological and functional heart remodelling. The lower RWT and better LV systolic and diastolic function are most likely positive echocardiographic findings.