Purpose This study evaluates the impact of a 3-week period of intensive pelvic floor muscles training (PFMT), with or without instrumentation, on clinical and static magnetic resonance imaging (MRI) changes of puborectalis (PR) and iliococcygeus (IL) muscles. Methods 24 healthy young women were enrolled in the study and 17 achieved the 9 sessions of 30 min training exercises and conducted all assessments. Participants were randomly assigned in two training groups: voluntary contractions combined with hypopressive exercises (HYPO) or biofeedback exercises combined with transvaginal electrical stimulations (ELEC). Clinical and T2-weighted MRI assessments were realized before and after training. Results Modified Oxford Grading System (MOGS) scores for left PR and perineal body significantly increased in the two groups (p = 0.039, p = 0.008), but MOGS score for right PR significantly increased only in HYPO (p = 0.020). Muscle volumes of right and left IL significantly decreased (p = 0.040, p = 0.045) after training as well as signal intensities of right and left PR (p = 0.040, p = 0.021) and thickness of right and left IL at mid-vagina location (p = 0.012, p = 0.011). Conclusions A short period of intensive PFMT induces clinical and morphological changes in PFMs at rest suggesting a decrease in IL volume and adipose content of PR. Although the results suggested that an intensive non-instrumented PFMT is as effective as an instrumented training, future controlled studies with greater sample sizes are needed to establish the relative and absolute effectiveness of each of the two interventions.