Conceptual understanding and motivation to learn are key factors in the success of biology learning. However, in biology lessons, the topic of bacteria is often considered difficult by pupils due to its abstract nature; consequently, teaching materials are required that can enhance pupil engagement in the learning process. This study seeks to investigate the enhancement of students’ conceptual understanding and learning motivation through the implementation of the MOEDU medium in learning about bacteria. A quantitative method was adopted in this research using a quasi-experimental Non-Equivalent Control Group design. The participants were drawn from two tenth-grade classes at State Senior High School 5 Tuban through a purposive sampling technique. Data collection was conducted using a conceptual understanding assessment and a questionnaire measuring students’ learning motivation. The collected data were analyzed employing the Mann–Whitney U test. The findings revealed an Asymp. Sig. (2-tailed) value of 0.000 (<0.05) from the Mann–Whitney U test, demonstrating a statistically significant difference between the experimental and control groups. The findings revealed an Asymp. Sig. (2-tailed) value of 0.000 (<0.05) from the Mann–Whitney U test, demonstrating a statistically significant difference between the experimental and control groups. In addition, students in the experimental class achieved an average learning motivation score of 77.13%, which was categorized as high, whereas the control class obtained an average score of 56.13%, categorized as moderate. Therefore, the implementation of the MOEDU medium contributed positively to enhancing students’ conceptual understanding and learning motivation in the study of bacteria.