It is widely demonstrated that moderate-intensity exercise is associated with improved fitness in non-communicable chronic diseases. However, there are no specific guidelines available for transplant recipients. Body composition is closely linked to exercise capacity, typically estimated by cardiopulmonary testing, but its potential correlation with cardiovascular health outcomes has not been investigated yet. This study aims to evaluate and compare cardiorespiratory performance and body composition in two groups of liver and kidney transplant recipients. A mixed group of transplant recipients (10 kidney and 15 liver) participating in a lifestyle reconditioning program through unsupervised physical exercise prescription was examined. Both groups were assessed using bioimpedance analysis (BIA), lifestyle, and physical activity levels by IPAQ questionnaire and cardiopulmonary testing (CPET). The two groups differed by IPAQ examination: liver transplant patients practiced more physical activity. Statistically significant differences were found in peak VO2/HR (oxygen pulse), which was higher in the kidney group compared to the liver group (15.63 vs. 12.49 with p < 0.05). Body composition did not show significant differences in BMI and the percentage of FM/FFM (FFM: 78.04 ± 7.7 in Kidney T vs. 77.78 ± 7.2 in Liver T). Systolic pressure measured at the peak was significantly higher in the liver group (162.6 vs. 134 with p < 0.01). The correlation between the CPET and BIA parameters showed a positive VO2 max and FFM mass trend. The results suggest differences in cardiorespiratory fitness between the two populations of solid organ transplant recipients despite not being related to the physical activity level. The data support the importance of body composition analysis in sports medicine and the prescription of physical exercise, especially considering the potential correlation with VO2 max, even though home-based exercise does not seem to alter it substantially. BMI does not appear to be a determinant of cardiovascular performance. Other determinants should be investigated to understand the differences observed.