Advances in physiology and other fields are strongly associated with a solid base knowledge of biochemistry and cell metabolism. On the other hand, the complex and abstract nature of metabolic pathways, the traditional lecture method, and other factors made the teaching-learning process of biochemistry a challenging endeavor. To overcome this, we developed and tested a novel active learning tool called Interactive Metabolism ( iM-tool). The iM-tool was developed with simple and low-cost materials. We used it for interactive teaching of several metabolic pathways and physiological mechanisms for students enrolled in the Biochemistry subject belonging to different undergraduate courses. The results of evaluation tests showed that the iM-tool significantly (ANOVA, P < 0.01) and consistently improved the biochemistry knowledge of students in classrooms with up to 50 students for 7 different and consecutive academic semesters. A survey intended to mine students’ opinions on the tools showed significant satisfaction with the teaching using the iM-tool over traditional lecture-based teaching, and the iM-tool contributed to collaborative learning among students. Therefore, our results showed that the iM-tool improves the biochemistry and cell metabolism teaching-learning process in a more attractive and interactive manner.