Instructors face challenges in facilitating higher levels of shared cognition in large enrolment classes. One strategy to foster shared cognition is the use of asynchronous discussions; however, these can be difficult to support with large numbers of students. Online protocols have been found to help students take more ownership of the discussion, reducing the workload of instructors and thus may be helpful in this context. The purpose of this study was to determine the most effective design of online protocols in large enrolment classes. The study used a design-based research methodology to iteratively design, assess and refine the online protocols and the design principles of its underlying protocol pedagogy. Participants for this study were 1,286 students enrolled in a blended undergraduate class in business that used online protocols for discussions over three semesters. The paper describes how iterative changes in the design of protocol-based discussions influenced students' cognitive presence. Students' perceptions of cognitive presence were significantly higher in the second and third iterations, and the concepts shared by group members were significantly more integrated by the third iteration. Findings suggest that with careful design, these enhanced protocols are a potentially useful strategy to facilitate asynchronous online discussions in large classes.