Combined functional training (FT), high-intensity interval training (HIIT) and aquatic exercise may improve health-related fitness in aging populations; however, the influence of baseline adiposity on training responses remains unclear. This study evaluated the effects of a 12-week multicomponent training program on aerobic capacity, body composition, metabolic health, and physical performance in middle-aged and older women and explored whether baseline body fat percentage modulated these responses. Thirty-four women (50–72 years) were assigned to a control group (Ctrl, n = 10) or an exercise group, stratified into normal fat (NF%, n = 10) and high fat (HF%, n = 14). The intervention included three weekly 60 min sessions consisting of HIIT, FT, and aquatic-based interval and resistance exercises, while controls maintained their habitual lifestyle without structured exercise. Significant improvements were observed in VO₂max, skeletal muscle mass, fasting insulin, triglycerides, total cholesterol, HDL cholesterol, and functional performance. Baseline adiposity influenced metabolic adaptations, with greater improvements in the HF% group. These findings suggest that multicomponent training may improve cardiometabolic health and physical performance; however, the results should be interpreted cautiously due to the quasi-experimental design and small sample size.