Pelvic floor muscles (PFMs) play a crucial role in urinary continence. Therefore, training the PFMs remains the most popular conservative treatment for urinary incontinence (UI). The effect of training other body muscles on the PFMs is unclear and mostly hypothetical. The objective of our study was to evaluate the effectiveness of postoperative diaphragm muscle, abdominal muscle and PFM training on PFM strength (PFMS) and endurance (PFME) as well as on UI in men after radical prostatectomy (RP). Per-protocol PFMS, PFME and urine loss measurements were performed at 1, 3, and 6 months postoperatively. The primary endpoints were PFMS and PFME differences among the study groups. The secondary endpoint was the correlation between UI and PFMS and PFME. In total, 148 men were randomized to the treatment groups. An increase in PFMS and PFME was observed in all groups compared to baseline (p < 0.001). The greatest difference in PFMS was in the PFM training group, but diaphragm training had the best effect on PFME. The highest (from moderate to strong) correlation between UI and PFME and PFMS (r = -0.61 and r = -0.89, respectively) was observed in the diaphragm training group. Despite different but significant effects on PFMS and PFME, all rehabilitation-training programmes decreased UI in men after RP.