For nearly two years, from 2020 to the first semester of 2022, massive full-time online learning was carried out. Currently, the online learning model is continuing to be used with the blended learning method, combining online and in-person classes. However, there is a lack of studies that focus on the experiences of English as a Foreign Language (EFL) learners in Indonesian higher educational institutions regarding teaching, social, and cognitive presences in online learning. Therefore, this study aimed to examine EFL learners' experiences with online learning using a cross-sectional survey involving 202 EFL learners from two Islamic universities in Indonesia who responded to the Community of Inquiry (CoI) questionnaire. The results of the study revealed that EFL learners had a positive perception of teaching and cognitive presence in online learning. However, they felt a negative social presence due to the lack of social interaction. Furthermore, the findings indicate that there were no significant differences in the perception of teaching, social, and cognitive presence over the length of the study and gender. Implications offer insights into the need for instructors to employ a variety of strategies to promote interaction and collaboration among learners and to focus on creating well-organized and structured courses that provide clear guidance and support for learners and promote active engagement with course materials.