<b><i>Introduction:</i></b> Research has consistently demonstrated that the COVID-19 pandemic, and resulting sudden shift to online learning (OL), had detrimental impacts on the motivation and mental health of university students. To date however this research has been cross-sectional and quantitative. <b><i>Method:</i></b> This study employed a mixed-methods design to examine the experiences of students at a large national Australian University both at the outset of the pandemic in 2020 (<i>n</i> = 824) and again 6 months later (<i>n</i> = 254) at the conclusion of their academic year. <b><i>Results:</i></b> Key findings from this study highlighted that despite quantitative findings suggesting poorer attitudes toward learning during the pandemic, qualitatively students perceived both positives and negatives to studying online. The qualitative results further highlighted that this experience was not the same for all and suggests the need to reconsider the standard approaches to offering support for students. <b><i>Conclusion:</i></b> Students reported poor mental health in both time points, but outlined avenues which improved not only their mental health but also their motivation for studying such as increased peer engagement and self-care activities. Students reported that OL negatively impacted on both their engagement with studies and their mental health, highlighting the need for universities to prioritize supporting their students’ mental health as much as their development of academic skills.