Background Students use mobile devices extensively in their everyday life, and the new technology is adopted in study usage. Since 2013, the University of Helsinki has given new medical and dental students iPads for study use. Simultaneously, an action research project on mobile learning started focusing on these students’ mobile device usage throughout their study years. Note taking is crucial in academic studies, but the research evidence in this area is scarce. The aims of this study were to explore medical and dental students’ self-reported study uses of mobile devices and their best practices of mobile note taking. Method An action research project began in 2013 and followed the first student cohort (124 medical and 52 dental students) with iPads from the first until the fifth study year. We explored students’ descriptions of their most important study uses of mobile devices and their perceptions of note taking with iPads. The longitudinal data were collected with online questionnaires over the years. The answers to open-ended questions were examined using qualitative content analysis. The findings were triangulated with another question on note taking and focus-group interviews. Results The response rates varied between 73 and 95%. Note taking was the most frequently and consistently reported study use of iPads during the study years. While taking notes, students processed the new information in an accomplished way and personalised the digital learning materials by making comments, underlining, marking images and drawing. The visual nature of their learning materials stimulated learning. Students organised the notes for retention in their personalised digital library. In the clinical studies, medical students faced the teachers’ resistance and ambivalence to mobile device usage. This hindered the full-scale benefit of the novel technology in the clinical context. Conclusions Efficient digital note taking practices were pivotal to students in becoming mobile learners. Having all their notes and learning materials organised in their personal digital libraries enabled the students to retrieve them anywhere, anytime, both when studying for examinations and treating patients in the clinical practice. The challenges the medical students met using mobile devices in the clinical setting require further studies. Electronic supplementary material The online version of this article (10.1186/s12909-019-1529-7) contains supplementary material, which is available to authorized users.