Given the rapid development of modern biotechnology, attention to socio-scientific issues in educational contexts is crucially important to support students in becoming responsible citizens. Our research focused on the impact of discussing socio-scientific issues during biology lessons under three different treatments (teacher-guided, student-centered, text-only), comparing these treatments with regard to cognitive achievement, cognitive load, and instructional efficiency. The biology lessons were part of an educational intervention with Bavarian 10th graders (N = 583) in an out-of-school laboratory on plant genetic engineering. The teacher-guided group performed significantly better regarding knowledge increase, while the cognitive load of the student-centered group was significantly higher. Accordingly, teacher-guided discussion led to the highest instructional efficiency, suggesting an enhanced cognitive achievement through the teacher’s guidance. However, a student-centered approach allows students to contribute more of their own opinions, making further research in this area desirable. Finally, we discuss potential implications for teaching and teacher education.