The sudden outbreak of COVID-19, which has presented great challenges to pedagogy, has catalyzed the transition of teaching and learning to the online mode. Uncovering the key factors that facilitate positive learning outcomes in online learning environments has thus gathered importance. To bring these factors to light, this study aims to understand and model the effect of perceived online connectedness on the relationship between student motivation and university learning outcomes. Based on 470 questionnaire responses collected by students from nine universities in Hong Kong and Macao, findings from structural equation modelling, showed students’ online connectedness partially mediated the relationship between online learning motivation and university learning outcomes. These results suggest that the learner’s motivation derives not only from the perceived relevance of the learning subject, but also from the learner’s attributes such as confidence, satisfaction, and attention during online learning. Moreover, students’ perceived connectedness, which considers the comfort, community, facilitation, interaction, and collaboration of students in an online context, plays a key role in students’ positive learning outcomes. Pedagogical implications for teachers, educators and students and university policy implications are discussed. Copyright © 2023 The Author(s), under exclusive licence to Springer Nature B.V.