In the current research study the use of Wikis as an online didactic tool to apply project-based learning in higher education was reported. The study was conducted in university teacher education programmes. During the online activities, participants developed interdisciplinary projects for the primary school working collaboratively in small groups in a Wiki virtual environment within the Moodle platform. Science was at the core of the projects and acted as an organising hub to finding links with other disciplines. A mixed-methods approach involving the collection of both quantitative and qualitative data was adopted in the current research study. The authors developed the following three instruments in order to measure both processes and outcomes of the online activities: the interdisciplinary project-based learning questionnaire, the reflection questionnaire and a rubric for assessing interdisciplinary projects. The current paper focuses only on the qualitative data, which were subjected to an inductive content analysis. Results provided evidence of the processes involved during the collaborative activities and that online activities can develop teachers' abilities to design projects in interdisciplinary contexts. The discussion highlights the aspects of the online environment that made the collaborative work effective in learning. Future implications and suggestions for teacher education programmes are discussed.