The purpose of this study was to examine the effects of a hypermedia learning environment on middle school students' meta-representational competence (MRC) in the domain of music. Particularly, we aimed at determining whether an educational intervention influenced the accuracy with which middle school students matched sounds (sonic fragments) to symbols (graphic representations). The students were randomly allocated to the experimental condition. An intervention was set up so that the experimental group students (E) were provided with scaffolding aimed at enhancing their use of constructive resources to generate representations and their critical capabilities to judge them. On the other hand, the control group students (C) followed a similar educational program lacking in such scaffolding. Both E and C groups were given the same pretest and posttest, which measured students' MRC by means of six representational criteria. One month after the posttest, a retention test took place. We hypothesized that the experimental program would have a positive overall effect on the students' MRC, which was partially supported, since such positive effect happened irrespective of the intervention. We also predicted a lasting effect of the intervention for the students who received scaffolding during the intervention, and that finding was also confirmed. As to the students' perception of the learning environment, the E group students overall scored their experience with the lesson in a more positive way than the C group, despite this trend was not confirmed for all the subscales of the survey. In addition, we inquired into the effectiveness of the treatment for participants with different levels of music experience, resulting an overall benefit from the intervention. As to the partial effect for the six representational criteria involved in the study, a significant overall effect because of the intervention was found for two non-epistemic criteria, namely formality and parsimony. Finally, regarding the partial effect for the three music parameters studied, a significant overall effect because of the treatment was found for pitch.