For decades of experience in teaching Chemistry, a chemical equation is usually balanced by writing a coefficient before the formula of atoms, ions, or molecules. In this study, the effect of a pedagogical intervention on the understanding and confidence of students was investigated by combining the guided-inquiry approach and the process of drawing of particles on balancing a chemical equation in a Philippine science classroom context. This action research gathered both qualitative and quantitative data in two phases. Initially, a three-tiered concept test determined the students' initial understanding and perceived confidence in balancing chemical equations using particulate drawings. The inquiry-based worksheets were implemented and investigated for its effectiveness. Specific cases from reflection responses and interviews were presented. The use of three-tiered tests and inquiry-based particulate worksheets exhibited significant change and a moderate positive correlation between conceptual understanding and confidence. This study was able to help Grade 11- STEM students improve their understanding and became more confident in learning the unseen particulate level of Chemistry concepts.