This 10-week randomized controlled trial investigates the effects of two different training modalities on hepatic fat content and cardiometabolic risk in sedentary postmenopausal women. Besides, alterations in physical fitness, hepatic fat content, and cardiometabolic risk will be associated with changes in those blood parameters that are usually modifiable by exercise training. Postmenopausal women (N = 32; ~61 years) were randomly assigned to one of the following treatment groups; (1) based on international exercise recommendations (EX group; n = 16), (2) exercise plus whole-body electromyostimulation (EX+EMS group; n = 16). Cardiometabolic risk score was calculated based on the international diabetes federation’s clinical criteria. Hepatic fat content was estimated using the fatty liver index. After the intervention, the cardiometabolic risk and the fatty liver index decreased, showing a higher impact on EX + WB-EMS. Physical fitness was assessed through aerobic and strength tests belonging to “Eurofit Testing Battery”. In all of them, significant differences were observed (p < 0.001), though EX+ EMS experienced better improvements (p < 0.05). In conclusion, a 10-week exercise training program, especially with WB-EMS, triggered improvements in physical fitness and reduced cardiometabolic risk and hepatic fat content in sedentary postmenopausal women.