Science learning motivation refers to the drive and enthusiasm that students exhibit towards learning science. Science learning competencies, on the other hand, are the skills and knowledge enabling students to understand and apply scientific concepts effectively. Digital literacy, defined as the ability to effectively use digital tools and resources, has emerged as a crucial skill in modern education. Digital literacy can bridge the gap between motivation and competencies by providing students with the tools they need to engage more deeply with scientific content. Given its significance, exploring the mediating role of digital literacy in the relationship between science learning motivation and competence is essential. Hence, we aimed to test the mediating role of digital literacy in the relationship between middle school students' science learning motivation and science learning competencies. To test these relations, we adopted the correlation design of the quantitative research method. The sample consisted of 471 middle school students. Science learning motivation scale, competence scale for learning science, and digital literacy scale were used to collect data. The hypothesis model was tested by using covariance-based structural equation modeling (CB-SEM). The results showed that science learning motivation is correlated with students' science learning competency (r = 0.891, p < 0.05) and digital literacy (r = 0.538, p < 0.05). Also, digital literacy partially mediates the relation between science learning motivation and science learning competency (r = 0.757, p < 0.05). These findings highlight the importance of fostering digital literacy in educational settings to enhance students' motivation and competency in science learning. Educators and policymakers should integrate digital tools and resources into the curriculum to create a more engaging and effective learning environment, thereby bridging the gap between students' motivation and their ability to master scientific concepts.