Background: The ageing process may lead to functional limitations, musculoskeletal pain, and worsened quality of life. The aim of this paper is to evaluate two physical therapy interventions for reducing musculoskeletal pain and improving quality of life in older adults. Methods: A cohort study was carried out with older people (60–75 years old). The Geriatric Physical Therapy group (n = 70) received massage therapy, therapeutic exercise, and therapeutic education program for 5 weeks; the Standardized Therapeutic Exercise group (n = 140) received a standardized therapeutic exercise and therapeutic education program for 3 weeks. Health-related quality of life (SF-36v2) and musculoskeletal pain intensity (VAS) were collected at baseline (A0), post-intervention (A1), and 12 weeks after baseline (A2). Results: There was pain intensity reduction in both groups (p < 0.05) and health-related quality of life improvement, except for Emotional Role (p = 0.34); Physical Function (p = 0.07), Bodily Pain (p = 0.02), and General Health (p = 0.09). At A2 there was a difference (p < 0.05) for neck pain in favor of the Geriatric Physical Therapy Group. Conclusions: Within the limitations of the study, it was possible to conclude that both physical therapy interventions showed a positive effect for reducing non-specific neck pain and low back pain in older adults, which may contribute to health-related quality of life improvement.