Teaching and learning in chemistry have been shifted to online classes due to the pandemic. With this, researchers investigated the use of multiple representations embedded to determine its effectiveness in online learning setup. A pretest-posttest with control quasi-experimental design was employed to two groups of Grade 11 STEM students taking up a general chemistry course in a private secondary institution in Cebu City, Philippines. The control group (n=30) was exposed to typical online class while the experimental group (n=30) was exposed to the multiple representations. Study findings revealed that there have been significant mean gains for both groups, indicating the important role of online learning in chemistry. The experimental group (MD=3.03, t=2.495, p=.015) had significantly higher mean gains than the control group, signifying the more effective nature of multiple representations in chemistry teaching. Moreover, the students had highly favorable attitudes towards multiple representations and had average extents of understanding in the macroscopic, microscopic, and symbolic levels. Therefore, the use of multiple representations promotes students’ chemical understanding during the Covid-19 pandemic. The researchers recommend the use of these representations in chemistry teaching, where teachers start at the macroscopic level before they proceed to the more abstract levels.