Secondary science education plays a key role in students’ process to become scientifically literate citizens. However, teaching students to acquire the necessary skills and knowledge to deal with complex societal issues is challenging. This paper reports about a study in which Scrum – a methodology to manage complex projects – was implemented in secondary chemistry classrooms to increase students’ conceptual understanding as well as their critical scientific literacy. A quasi-experimental design was used with 198 Grade 11 students from eight different classes. The experimental condition (99 students, 4 classes, 25 groups with 3 or 4 students, 2 teachers) used Scrum methodology during a context-based course on Green Chemistry. The comparison condition (99 students, 4 classes, 29 groups of 3 or 4 students, 3 teachers) completed the same module about Green Chemistry, without using Scrum methodology. At the end of the course students formulated a written advice on the greenest synthesis of adipic acid. A pre-test on prior knowledge of Green Chemistry principles and a post-test on conceptual understanding of the chemistry concepts involved were administered. In addition, the Standard Observed Learning Outcomes taxonomy (SOLO) was used to analyse the quality of the written advices as a measure for students’ critical scientific literacy. Students from the experimental condition outperformed their peers from the comparison condition in their conceptual understanding. Moreover, the quality of the advices of students from the experimental condition were rated higher than the quality of advices of students in the comparison condition. These findings are discussed and connected to Scrum methodology as teaching approach to scaffold both students’ conceptual understanding and its potential to promote the development of their critical scientific literacy.