The main objective of this pilot study was to evaluate the effects of functional exercise training (FET) and home exercise training (HET) on body composition, cardiometabolic risk factors, muscle strength, and functional capacity in individuals with bariatric surgery. The sample of the study included 30 individuals who underwent bariatric surgery. The FET group had functional exercise training consisting of stretching, aerobic, strengthening, and balance exercises assigned by a physiotherapist (n = 15), and the HET group had the same exercises under supervision (n = 15). The training sessions were planned as × 3 per week for a period of 8 weeks. Body composition, cardiometabolic risk factors, cardiometabolic risk status, muscle strength, and functional capacity of all individuals were evaluated before and after training. According to the measurements, body weight (BW), body mass index (BMI), body fat mass (BFM), C-reactive protein, glycated hemoglobin, insulin resistance, cardiovascular risk total score, and ten-year cardiovascular percentage risk decreased significantly ( < 0.05), while HDL-C, leg, back, and hand grip strength (right-left), and walking distance increased significantly ( < 0.05) in the FET group. In the HET group, there were significant increases in body fat percentage (BFM %), BFM, and body muscle mass percentage (BMM %) ( < 0.05), while body muscle mass (BMM), right hand grip strength, leg and back muscle strength, and walking distance scores significantly decreased ( < 0.05). It was concluded that personalized and supervised FET has a positive effect on body composition, cardiometabolic risk factors, muscle strength, and functional capacity, and it can be recommended as a safe exercise model for bariatric surgery patients.