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Background: The aging society worldwide carries public and inevitable issues. Aging is accompanied by multiple diseases, and the health impacts challenge healthcare and social systems. In addition to medical treatment, exercise has been recognized as an effective strategy not only for disease prevention and alleviation, but also for multiple health benefits on health promotion. The purpose of this study was to investigate the effects of a suitable Pilates exercise intervention program on health maintenance and benefits in community-dwelling middle-aged women with a quasi-experimental design. Methods: We recruited healthy middle-aged community-dwelling women who had not regularly exercised in the previous three months. The participants were assigned to the experimental (n = 22) and control (n = 23) groups based on a quasi-experimental design. The experimental group participated in a mat-based Pilates exercise class twice a week (1 h/session) throughout the 12-week intervention, whereas there was no intervention for the control group. Body composition, basal metabolic rate, and functional physical fitness—comprising cardiovascular capacity, flexibility, muscular strength of upper limbs, muscular strength of lower limbs, core strength, agility, static balance, and dynamic balance—were assessed as primary outcomes in both groups before and after the intervention. Results: There were no significant differences in any of the dependent variables between the two groups before the exercise intervention. After the 12-week intervention, body composition, including body mass index, body fat (−1.5 to 3%), and basal metabolic rate (+10.6%), and functional fitness, including flexibility (+3.5%), core strength (+31.5%), lower-limb strength (+13.5%), agility (+7.3%), and balance (+4.2%), improved significantly in the experimental group relative to the control group (p < 0.05). Moreover, the improvement in physical fitness in lower-limb strength, agility, and balance for fall prevention also demonstrated higher clinical significance than the control. Conclusions: This 12-week mat-based Pilates exercise program significantly improved body composition, basal metabolic rate, and functional physical fitness in community-dwelling middle-aged women. The beneficial effects of Pilates exercise programs may thus promote improved health in the middle-aged female population, with practical implications for communities.