To evaluate changes in joints after physiotherapy in post-menopausal women, specifically to identify clinical responses to the measurements of flexibility, functional capacity and joint pain in early and late post-menopausal women at a multi-disciplinary health education programme. A total of 69 women participated in the Integral Program for the Attention to Climacteric Women at the Department of Gynecology - Federal University of Sao Paulo and were sorted into two groups of early (n = 32) and late (n = 37) post-menopause. The average age of menopause was 47.9 ± 5.6 years. The Blatt Kupperman Menopausal Index scores for the early (baseline = 12.8 ± 6.1) and late (baseline = 14.1 ± 7.7) post-menopausal groups after the programme were 8.4 ± 7.1 and 9.4 ± 8.1, respectively. Both groups presented improvements regarding functional capacity (p < 0.01) and complaints of pain (p < 0.001) after the intervention. The group of early post-menopausal women had better flexibility for hip flexion (p < 0.001), and the late post-menopausal group showed greater improvement in shoulder flexion (p < 0.001), extension (p < 0.001) and elbow flexion (p < 0.001). After multi-disciplinary approach, both early and late post-menopausal groups experienced decrease in intensity of climacteric symptoms, reduction in pain intensity and improvement in functional capacity, but the flexibility was different between both the groups.