Metabolic flexibility includes the ability to perform fat and carbohydrate oxidation, as well as oxidative capacity, which is associated with mitochondrial function, energetic contributions, and physical health and performance. During a session of graded incremental exercise testing (GIET), we investigated metabolic flexibility, the contributions of three energy systems, and performances of individuals with different metabolic characteristics. Fifteen general population (GP; n = 15, male n = 7, female n = 8) and 15 national-level half-marathon and triathlon athletes (A; n = 15, male n = 7, female n = 8) participated in this study. During GIET, heart rate (HR), oxygen uptake (V˙O2mean and V˙CO2mean), metabolic equivalents (METs) in V˙O2mean, and blood glucose and lactate concentrations (La−) were measured. Furthermore, jogging/running speeds (S) at specific La−, fat and carbohydrate oxidations (FATox and CHOox), and energetic contributions (oxidative; WOxi, glycolytic; WGly, and phosphagen; WPCr) were calculated. The percentages of HRmax, relative V˙O2mean, V˙CO2mean, and METs in V˙O2mean were all lower in A than they were in GP. FATox values were lower in GP than in A, while CHOox and La− were higher in GP than in A. Negative correlations between La− and FATox were also observed in both groups. Contributions of WOxi, WGly, and WPCr were higher in GP than in A during GIET. Moreover, values of WGly, and WPCr were significantly lower and higher, respectively, in male GP than in female GP. Furthermore, S at specific La− were higher in A than in GP. It is suggested that an individualized low-intensity recovery exercise program be established, to achieve increased metabolic flexibility and oxidative capacity (aerobic base), such as public health improvements and a greater volume of higher exercise intensities; this is the type of exercise that elite athletes worldwide mostly perform during their training period and progression. This may prevent cardiac/metabolic diseases in GP.