The worldwide disruption of higher education during the Covid-19 pandemic has been studied from the viewpoints of institutions and teachers, with some attention to students’ health and learning challenges. Attempts to theorise the diverse and conflicting challenges faced by students learning online during the pandemic have been limited. It is helpful to analyse students’ experiences as part of an activity system in order to unravel the system’s elements and determine contradictions that occur. This study adopted a mixed methods approach to investigate students’ online learning experiences at all eight New Zealand universities during the pandemic. Data obtained via a large-scale online survey, followed by focus groups and individual interviews, is presented in light of an Activity Theory framework. Findings show that students’ key challenges were associated with new tools and technologies, lack of interaction and social connection, lack of routine and space, and clashing commitments due to multiple roles and responsibilities. Contradictions can be a driving force for change and development in teaching and learning contexts. We conclude with recommendations for tertiary institutions, teachers, learning designers and students to inform future learning and teaching plans.