This paper presents a mixed methods study in which 77 students and 3 teachers took part, that investigated the practice of Learning by Design (LBD). The study is part of a series of studies, funded by the Netherlands Organisation for Scientific Research, that aims to improve student learning, teaching skills and teacher training. LBD uses the context of design challenges to learn, among other things, science. Previous research showed that this approach to subject integration is quite successful but provides little profit regarding scientific concept learning. Perhaps, when the process of concept learning is better understood, LBD is a suitable method for integration. Through pre- and post-exams we measured, like others, a medium gain in the mastery of scientific concepts. Qualitative data revealed important focus-related issues that impede concept learning. As a result, mainly implicit learning of loose facts and incomplete concepts occurs. More transparency of the learning situation and a stronger focus on underlying concepts should make concept learning more explicit and coherent.