The emergence of COVID-19 in 2020 forced the whole world to a standstill for a while, causing open and distance e-learning institutions like Unisa to adjust all teaching and learning activities and shift to online teaching entirely. This study explores the online learning challenges students in an open and distance e-learning environment in South Africa experienced during the COVID-19 pandemic, as guided by the Community of Inquiry framework. This qualitative content analysis study used thirty honours students' responses to an open-ended question. Participants could share any thoughts on collaborative learning in an online environment. The key challenges identified by participants were the lack of teacher feedback, communication, online discussion, and interaction linked to teaching presence. The cognitive difficulties include complex modules, challenging questions, and a lack of detailed feedback. The social presence challenges indicated a lack of online support, virtual interaction, and online participation by teachers-to-students and student-to-peer-students. The study recommends the importance of teachers incorporating various facilitation strategies using the Community of Inquiry framework to create an effective online learning environment to assist students in studying remotely.