The purpose of this study was to understand how the use of multiple representations (MR), during a sequence of lessons on the saponification reaction, can help students develop their cognitive structures. We examined (i) the effect of the teaching sequence with MR on the development of the students' cognitive structures and (ii) how, according to the students, that sequence helped them to develop their cognitive structures. This study was conducted in three Grade 12 classes, including a total of 68 students. This study follows a pre-experimental one group pretest-posttest design, providing an intervention during the experiment. We used two data collection instruments: a Word Association Test (WAT) and a focus group interview. The results obtained from the WAT show that the students' cognitive structures progressed from the pretest to posttest, with an increase in the number of response words and connections between words, and with a change in the nature of these connections. The results suggest that this development was influenced by the way students used MR, making use of the three MR functions proposed by Ainsworth (2006, 2008). The students recognized that the combination of the three MR functions allowed them to move across representation levels (macroscopic, symbolic and submicroscopic) and to develop a deeper and more structured understanding of the concepts related to the saponification reaction.