This 12-week randomized controlled trial investigates the effects of different training modalities on cardiometabolic risk in sedentary, middle-aged adults, and examines whether alterations in cardiometabolic risk are associated with changes in those health-related variables that are modifiable by exercise training. The study subjects were 71 middle-aged adults (~54 years old;~50% women) who were randomly assigned to one of the following treatment groups: (1) no exercise (control group), (2) concurrent training based on international physical activity recommendations (PAR group), (3) high intensity interval training (HIIT) group, or (4) HIIT plus whole-body electromyostimulation (HIIT+EMS group). A cardiometabolic risk score was calculated based on the International Diabetes Federation's clinical criteria. A significant reduction in cardiometabolic risk was observed for all exercise training groups compared to the control group (all p < 0.05), which persisted after adjusting potential confounders (all p < 0.05). However, the HIIT+EMS group experienced the most significant reduction (p < 0.001). A significant inverse relationship was detected between the change in lean mass and the change in cardiometabolic risk (p = 0.045). A 12-week exercise training programs-especially the HIIT+EMS program-significantly reduced cardiometabolic risk in sedentary, middle-aged adults independent of sex, age, and cardiorespiratory fitness.