Prior research has revealed resistance against wiki collaboration in higher education classrooms. Compared with small-group projects, whole-class knowledge building (KB) on a wiki is difficult, given students' lack of similar experiences, which requires scaffolding intersubjectivity and transfer of responsibility. This paper focuses on the second cycle of a design-based research study to develop learner autonomy in wiki-supported KB. A learner autonomy framework guided the re-design of the instructional theory with content from the relevant literature. The theory was implemented in an undergraduate design course to validate and refine the theory. We analyzed the data from observations, wiki content, interviews with the expert instructor and two other instructors and a focus-group interview with students. We found that the KB principles helped students understand KB; and the self-regulation and meta-cognition strategies increased motivation and confidence in KB. From the success of this case, we propose that scaffolding learner autonomy for a wiki-supported KB calls for a change in students' learning mindsets and requires careful instructional design to support the cognitive, behavioral and affective aspects of change to reduce resistance.