We aimed to investigate the effects of different exercise training programs on body composition parameters in sedentary middle‐aged adults. A total of 89 middle‐aged adults (53.5 ± 4.9 years old; ~53% women) participated in the FIT‐AGEING study. A 12‐week randomized controlled trial was performed with a parallel group design. The participants were randomly assigned to (a) a concurrent training based on physical activity recommendation from the World Health Organization group (PAR group), (b) a high‐intensity interval training group (HIIT group), and (c) a high‐intensity interval training group adding whole‐body electromyostimulation group (WB‐EMS group). A significant decrease of fat body mass, fat body mass index, and visceral adipose tissue was observed in all training modalities compared to the control group (all P ≤ 0.001). There was a significant increase in lean body mass in the HIIT group as well as in the WB‐EMS group compared to the control group and the PAR group (all P ≤ 0.044), whereas an increment of lean body mass index was only observed in the WB‐EMS group compared to the control group and the PAR group (all P ≤ 0.042). A significant increase of bone mineral content was observed in the WB‐EMS group compared to the control group (P = 0.015), while no changes were found in the PAR group and in the HIIT group compared to the control group (all P ≥ 0.2). Our findings suggest that PAR, HIIT, and WB‐EMS can be used as a strategy to improve body composition parameters, obtaining slightly better results with the application of WB‐EMS.