Science education plays a pivotal role in shaping the nation’s future, but then science is tagged as one of the difficult subjects to learn. This difficulty stemmed from the abstract nature of science which concepts such molecular competencies are not directly observable in class which makes it even harder for students to grasp. This study evaluates the effectiveness of an e-SIM for enriching the least learned competencies in Biology specifically Deoxyribonucleic acid (DNA), protein synthesis, and mutation. The evaluation of the e-SIM asserted its potential as a supplemental digital tool. The results of the study indicate that the posttest scores of the students have significantly improved after the utilization of e-SIM as supported by the t-test result. This concludes that the e-SIM holds a great potential for enriching science learning, improving academic performance and the students’ learning experience.