E-portfolios have been adopted by higher education institutions as assessment for learning tools to develop students' reflective thinking and their ownership of learning. This paper examines how e-portfolios are integrated in an undergraduate course at a Hong Kong university to develop students' reflective thinking. Based on the qualitative data collected and analysed from both the teacher and students in the course, this paper first discusses the different levels of reflective thinking that the students developed as they were working on their e-portfolios. It then identifies the factors that facilitate and hinder students' development of reflective thinking, how the facilitating factors are enabled and what the hindering factors need to be addressed. These key findings highlight the pivotal role of the teacher as a learning facilitator and guide, the scaffolding role of the toolkit to support both teachers and students, and the necessity of the technical capacity building and support in the implementation of e-portfolios in higher education. Copyright © 2020 Springer Nature.