Teaching and learning in universities have shifted towards online education, and there is not enough scientific knowledge about suitable pedagogical design principles to guide the construction of hybrid learning spaces for today’s university students. In this design‐based research, we studied the benefits and challenges in reaching the expected learning outcomes of an e‐course, “Collaboration and Professional Interaction Skills.” The practical purpose was developing the pedagogical design of this e‐course. The scientific objective was to build on the research about design principles that guide teachers in constructing e‐courses, enabling in‐depth learning in hybrid learning spaces. The pedagogical design was guided by six design principles. Empirical data (21 students’ assignments and reflections, teacher’s observations, data from the digital learning management system) were collected in two research cycles. Students were from different degree programmes of educational sciences. Thematic analysis of students’ individually and collaboratively authored assignments was carried out in both research cycles. The most emphasised benefits and challenges concerned the combination of working and creating knowledge together, virtually, in a multidisciplinary group. Based on the results, practical recommendations were made for university‐level pedagogical designs that facilitate effective and active collaboration and interaction, and learning of such competence. What is already known about this topic: In higher education, more emphasis needs to be placed on learning skills such as multidisciplinary teamwork and collaborative knowledge creation. There is a need for more personalised learning opportunities that offer flexibility in one’s studies and take learners’ diverse situations into account. Advanced understanding of suitable pedagogical design principles and knowledge from empirical cases is needed. What this paper adds: What to consider when technology is used to mediate the learning processes. How to tackle the demands of personalised study opportunities and demanding interaction skills by online collaboration. Implications for practice and/or policy: Pedagogical design exemplifying how students build shared knowledge objects iteratively. Students need guidelines and support for multidisciplinary collaboration and interaction online. Learning management systems are not fully tailored for iterative multidisciplinary collaboration; thus, the designer of the course must be aware of the limitations and develop ways of overcoming the discrepancies between the learning management system and learning objectives.