Using socio-scientific issues as a learning context is an effective approach to achieve an important goal in science education, which is to enhance scientific literacy. It involves strengthening skills such as argumentation while also improving an understanding of the Nature of Science and imparting content knowledge. The present study evaluates the impact of a web-based educational instrument consisting of a unique combination of features designed to promote students’ development of skills and knowledge as well as to address the challenges faced by teachers in teaching socio-scientific issues. Participants included 423 students in secondary education. Students in the experimental condition received a three-lesson intervention with the educational instrument, and students in the control condition followed their regular science lessons. Findings indicated that the instrument proves effective in fostering learning outcomes while teachers benefit from the shift of managing classroom discussion to individual guidance of students. Applying the educational instrument in the classroom demonstrates promise in improving student engagement and their comprehension of socio-scientific issues.