This study aims to investigate what and how Taiwanese EFL university students write in their English academic lecture notes. In addition, this study also aims to examine the roles of lecture discourse signaling cues in the organization of EFL students’ lecture note-taking. The participants of this study include 24 EFL university or graduate school students enrolled in an academic listening course in a national university in Taiwan. All of the participants have an English proficiency level of B2 to C1 under the framework of the Common European Framework of Reference for Languages. To find out what the participants write in and how they organize their academic lecture notes, the participants are asked to listen to a 10-to-15-minute long mini-lecture with discourse signaling cues each week in class. The lecture notes are then collected for analysis. Analysis of the students’ lecture notes reveals several findings: (1) the students have learned to use keywords and organizational structure in their lecture notes; (2) the quality of students’ lecture notes has improved; (3) the students have learned to use discourse signaling cues to retain detailed information such as examples and definitions in their notes. Based on the findings, this study suggests that, in order to improve academic listening skills, it is essential to develop note-taking skills with lecture discourse signaling cues for EFL students in Taiwan.