In Community-Based Participatory Research (CBPR), people with shared lived experiences (co-researchers) identify priority needs and work collaboratively to co-design an action-oriented research advocacy project. For this to occur, academic researchers must build mutually respectful partnerships with co-researchers by establishing trust. In the context of the COVID-19 pandemic, our objective was to virtually assemble a group of co-researchers (people with diverse but relevant experiences of homelessness and diabetes) and academic researchers who engaged in the CBPR process to identify a project that would address the difficulties of diabetes management while experiencing homelessness. Co-researchers were recruited to the committee from community homeless-serving organizations. Six co-researchers, one peer researcher and three academic researchers from Calgary, Alberta met virtually for bi-weekly committee meetings, from June 2021 to May 2022 to explore barriers to diabetes management and to complete a priority-setting exercise to determine the focus of our collective project. After reflecting on our virtual CBPR experience we present lessons learned related to: i) technical challenges and logistical considerations, ii) meeting virtually and building rapport, iii) driving engagement, and iv) challenges of transitioning from virtual to in-person meeting format. Overall, the process of conducting a CBPR project virtually to engage a group of co-researchers during a pandemic presents its challenges. However, a virtual CBPR project is feasible and can lead to meaningful experiences that benefit all group members, both from the community and academia.Supplementary InformationThe online version contains supplementary material available at 10.1186/s40900-023-00456-z.