This study aimed to compare the effects of Zumba and Pilates training on functional performance, mood, and health-related quality of life in postmenopausal women. Fifty-four postmenopausal women, aged 55–65, were randomly allocated to a control group (CG), a Pilates group (PG), or a Zumba group (ZG). Functional performance factors, in terms of walking speed, lower body muscle strength, dynamic balance, and functional mobility, as well as mood and health-related quality of life (HRQoL), were assessed before and after the intervention period. As results, both training modalities significantly improved the walking speed (PG (p < 0.001)/ZG (p < 0.001)), strength (PG (p < 0.001)/ZG (p < 0.05)), dynamic balance (PG (p < 0.001)/ZG (p < 0.001)), and functional mobility (PG (p < 0.001)/ZG (p < 0.001)), as well as mood (PG (p < 0.01)/ZG (p < 0.001)). Additionally, both intervention programs significantly improved their HRQol [physical function (PG (p < 0.001)/ZG (p < 0.001)) domain and SF36 total scores (PG (p < 0.01)/ZG (p < 0.001))] with better performance following Zumba training. However, the domains of social function (p < 0.001), mental health (p < 0.001), and role limitation due to emotional problems (p < 0.05) significantly enhanced only for the ZG. In conclusion, Pilates or Zumba training appears to be an ideal exercise for promoting functional performance, mood, and HRQoL in postmenopausal women. However, Zumba training seems to be more effective, resulting in optimal scores.