Adopting a mixed methods approach, this study examined the relationships between undergraduate students' motivation, engagement and learning outcomes during the COVID-19 pandemic. An online questionnaire survey was administered to collect quantitative and qualitative data. A sample of 10,060 undergraduates from 23 universities in China participated in the survey. The results of quantitative analyses largely confirmed the hypothesised relationships between students' motivation, engagement and the two learning outcome indicators (i.e. mastery of generic skills and overall satisfaction). The qualitative analyses not only supported the quantitative findings, but also identified four types of learning outcomes of online learning emerging from the data. The results indicated that emergent online learning had a favourable influence on students' learning strategies, but had mixed or negative effects on their learning effectiveness, attitudes and emotions. The qualitative results revealed eight major factors that facilitated or hindered students' engagement in online learning during the pandemic. These findings contribute to the conceptualisation and measurement of student engagement in online learning, and emphasise the need to conduct mixed methods research in different learning contexts. The implications for improving online learning and teaching in higher education are discussed.