Lately, chairs have been widely used as a cheap, easily accessible, safe, and effective training means in different settings (e.g., in gyms, the house, workplaces, and in rehabilitation). This study investigated the effectiveness of a 10-week chair-based music–kinetic integrated combined exercise program on health, functional capacity, and physical fitness indicators of middle-aged pre-menopausal women. A total of 40 healthy women (40–53 years) were assigned to two groups: exercise (EG) and control (CG). The EG followed a 10-week (3 times/weekly; 30 training sessions) chair-based exercise program including aerobic dance, flexibility, coordination, and strength exercises with body weight or auxiliary means. Selected indicators of health, functional capacity, and physical fitness were evaluated before and after the 10 weeks. Following the program, the EG significantly reduced their body fat (−2.5%), blood pressure (by −4.5 to −5.5%), the time during the timed up-and-go (TUG) test (by −10.27%), heart rate (by −6.35 to −13.78%), and the rate of perceived exertion (by −24.45 to −25.88%), while increasing respiratory function (3.5–4%), flexibility (12.17%), balance (50.38–51.07%), maximal handgrip strength (10–12.17%), and endurance strength (43.87–55.91%). The chair-based combined music–kinetic exercise program was effective and could be safely used in different settings to improve health, functional capacity, and physical fitness in middle-aged women.