Objective To compare effects and cost‐effectiveness of pelvic floor muscle training ( PFMT ) and watchful waiting in women with pelvic organ prolapse. Design Randomised controlled trial. Setting Dutch general practice. Population Women (≥55 years) with symptomatic mild prolapse, identified by screening. Methods Linear multilevel analysis. Main outcome measures Primary outcome was change of pelvic floor symptoms (Pelvic‐Floor‐Distress‐Inventory‐20 [ PFDI ‐20]) during 24 months. Secondary outcomes were condition‐specific and general quality of life, costs, sexual functioning, prolapse stage, pelvic floor muscle function and women's perceived improvement of symptoms. Results PFMT ( n = 145) resulted in a 12.2‐point (95% CI 7.2–17.2, P < 0.001) greater improvement in PFDI ‐20 score during 24 months compared with watchful waiting ( n = 142). Participants randomised to PFMT more often reported improved symptoms (43% versus 14% for watchful waiting). Direct medical costs per person were €330 for PFMT and €91 for watchful waiting but costs for absorbent pads were lower in the PFMT group (€40 versus €77). Other secondary outcomes did not differ between groups. Post‐hoc subgroup analysis demonstrated that PFMT was more effective in women experiencing higher pelvic floor symptom distress at baseline. Conclusion PFMT resulted in greater pelvic floor symptom improvement compared with watchful waiting. The difference was statistically significant, but below the presumed level of clinical relevance (15 points). PFMT more often led to women's perceived improvement of symptoms, lower absorbent pads costs, and was more effective in women experiencing higher pelvic floor symptom distress. Therefore, PFMT could be advised in women with bothersome symptoms of mild prolapse. Tweetable abstract Pelvic floor muscle training can be effective in women with bothersome symptoms of mild prolapse.