Hypopressive exercises have emerged as a conservative treatment option for pelvic floor dysfunction (PFD). The aim of this study was to compare the effects of an eight-week hypopressive exercise program to those of an individualized pelvic floor muscle (PFM) training (PFMT) program, and to a combination of both immediately after treatment and at follow-up assessments at 3, 6 and 12 months later. The study was a prospective, single-centre, assessor-blinded, randomised controlled trial. Ninety-four women with PFD were assigned to PFMT (n = 32), hypopressive exercises (n = 31) or both (n = 31). All programs included the same educational component, and instruction about lifestyle interventions and the knack manoeuvre. Primary outcomes were the Pelvic Floor Distress Inventory Short Form (PFDI-20); the Pelvic Floor Impact Questionnaire Short Form (PFIQ-7); PFM strength (manometry and dynamometry) and pelvic floor basal tone (dynamometry). There were no statistically significant differences between groups at baseline, nor after the intervention. Overall, women reduced their symptoms (24.41-30.5 on the PFDI-20); improved their quality of life (14.78-21.49 on the PFIQ-7), improved their PFM strength (8.61-9.32 cmH2O on manometry; 106.2-247.7 g on dynamometry), and increased their pelvic floor basal tone (1.8-22.9 g on dynamometry). These data suggest that individual PFMT, hypopressive exercises and a combination of both interventions significantly reduce PFD symptoms, enhance quality of life, and improve PFM strength and basal tone in women with PFD, both in the short and longer term.