Background: There is still no consensus on the most suitable interventions for exercise practice in breast cancer survivors. Therefore, the aim of this study was to evaluate the effect of a two-year physical activity intervention (strength, aqua fitness and aerobic exercise programs) on the self-perceived quality of life and physical functionality of female breast cancer survivors. Methods: A randomized, controlled, experimental trial with a sample of 316 women (63 ± 7 years), who had been diagnosed with breast cancer. The evaluations were performed using the Rikli & Jones Senior Fitness Test, and the Short Form 12 Health Survey (SF-12). Results: The participants in the strength program showed statistically significant improvements in all the items of the SF-12. The aqua fitness program obtained significant improvements in Physical Functioning and Limitations, Pain and Emotional Limitations, General Health, Vitality, Social Functioning and the physical and mental components of the SF-12. The participants in the aerobic program showed a progressive deterioration of Vitality and Mental Health. Conclusion: When assigning breast cancer survivors to an exercise program, the preferential or predominant activity should include strength exercises. On the other hand, as the second choice, those patients with particularly low levels of Vitality or Physical Limitations will show greater improvement with an aqua fitness program.