This paper presents a mixed methods study in which 21 first-year student teachers took part that investigated learning outcomes of a modified learning by design task. The study is part of a series of studies that aims to improve student learning, teaching skills and teacher training. Design-based science challenges are reasonably successful project-based approaches for breaking down the boundaries between traditional school subjects. Previous learning outcomes of the extensively studied Learning by Design (LBD) approach demonstrated a strong positive effect on students’ skills. However, compared to traditional classroom settings, LBD provided little or no profit on (scientific) concept learning. For this, according to two preliminary studies, a lack of explicit teaching and scaffolding strategies, both strongly teacher-dependent, bears a share of responsibility. The results of this third study indicate that more emphasis on these strategies indeed strengthens concept learning without reducing positive effects on skill performance.