Teaching with Scrum methodology includes ceremonies, roles and artefacts supporting students in planning, monitoring and directing their learning process. It scaffolds students' learning in complex and sometimes overwhelming context-based learning environments. Effects of the implementation on both students' learning outcomes and self-reported perceptions of six affective and metacognitive outcomes were investigated. Six teachers implemented Scrum methodology in a context-based secondary chemistry module on Green Chemistry. Their classes formed the experimental group. Based on how students experienced the quality of the implementation, teachers of the experimental group were subdivided into top-teachers and growth-teachers. Consequently, their students formed two sub-experimental groups. The comparison group, which did not use Scrum methodology, consisted of students taught by four teachers. A pre-test post-test control group design was used to study its effect on students' achievements and self-reported affective and metacognitive outcomes. Students of both experimental groups outperformed students of the comparison group with a large effect-size (top-teachers); and medium effect-size (growth-teachers) on learning outcomes. Findings on students' perceptions of affective and metacognitive outcomes revealed medium and small effects of Scrum methodology. Despite the fact that the implementation is challenging for teachers, it appears that Scrum methodology has positive effects on students' achievement and on students' perceptions of affective and metacognitive dimensions of their learning.