Purpose In response to the evolving COVID-19 pandemic, many universities have transitioned to online instruction. With learning promising to be online, at least in part, for the near future, instructors may be thinking of providing online collaborative learning opportunities to their students who are increasingly isolated from their peers because of social distancing guidelines. This paper aims to provide design recommendations for online collaborative project-based learning exercises based on this research in a software engineering course at the university level. Design/methodology/approach Through joint work between learning scientists, course instructors and software engineering practitioners, instructional design best practices of alignment between the context of the learners, the learning objectives, the task and the assessment are actualized in the design of collaborative programming projects for supporting learning. The design, first segments a short real-time collaborative exercise into tasks, each with a problem-solving phase where students participate in collaborative programming, and a reflection phase for reflecting on what they learned in the task. Within these phases, a role-assignment paradigm scaffolds collaboration by assigning groups of four students to four complementary roles that rotate after each task. Findings By aligning each task with granular learning objectives, significant pre- to post-test learning from the exercise as well as each task is observed. Originality/value The roles used in the paradigm discourage divide-and-conquer tendencies often associated with collaborative projects. By requiring students to discuss conflicting ideas to arrive at a consensus implementation, their ideas are made explicit, thus providing opportunities for clarifying misconceptions through discussion and learning from the collaboration.