Design-based research is an approach frequently applied in research projects that examine technology-enhanced learning environments in real-world settings. This is important if we are to arrive at solutions that support authentic learning contexts. However, as researchers in such a project, there are challenges. While design-based research supports the way we think about design as process and as artifacts, we often struggle with issues not always directly connected, but definitely linked, to our design-based research approach. In this paper, we retrospectively reflect on emergent lessons from our 12-year experience in a design-based research project to develop a technology-enhanced learning environment for large university classes. We discuss some of the issues we experienced and still have to deal with repeatedly while working towards implementing and improving our learning design in large university courses. The discussion and insights in this paper are designed as signposts for researchers in the area that might provide direction, support and, foremost, a basis for further discussion.