The COVID-19 pandemic has introduced challenges to delivering laboratory-based STEM curricula. This study evaluates students’ learning experience in a synchronous team design activity within the laboratory component of an undergraduate Computer Engineering course during the pandemic. Using the EduPad digital platform, students collaborated in small groups to develop a working design for a software simulator. The researchers measured students’ social, cognitive, and teaching presences during the remote team design activities and gathered their feedback on the learning experience. The findings demonstrate that students exhibited high levels of cognitive presence during the remote team design activities, suggesting effective strategies for promoting cognitive presence in synchronous engineering laboratory instruction. This study contributes to the community of inquiry framework and expands the existing repertoire of techniques for enhancing cognitive presence in online synchronous instruction. The implications for further research are also discussed.