The global outbreak of COVID-19 has resulted in the most significant disruption to education systems in history, impacting educators and students across a range of educational institutions from primary to tertiary level (United Nations, 2020). The lockdown has resulted in a significant shift in learning methods from in-person instruction to online learning, with some institutions even closing as a result of the suspension of classes. The research intended to determine the perceptions of allied medical course students towards online learning, to find their reaction to the transition from face-to-face to online implementation of classes, perceived advantages and disadvantages, and their overall preference based on their experience during the COVID-19 pandemic. The study used a descriptive qualitative research design and is deemed appropriate since the study 135 Ignatian International Journal for Multidisciplinary Research Vol 2 No 1 January 2024 www.icceph.com aimed to find out the perceptions of the Bachelor of Medical Laboratory Science students about online learning during the onset of the COVID-19 pandemic. The study has unraveled the initial reaction of the BMLS Students to Online Classes such that (1) Students were excited and; (2) worried; (3) Some students remained neutral. On the other hand, Students' Perceptions about Online Learning can be Advantageous and have unearthed the following themes: (1) it is more flexible (2) it is convenient (3) it allows students to study at their own pace (4) it gives them the comfort of studying at home ; (5) it reduces risk of COVID-19 transmission as well as Disadvantageous where the students perceived online learning as disadvantageous as (1) it highly requires a stable internet connection (2) it is uncomfortable to communicate online (3) it negatively affects the study habits or lifestyle of students (4) it encourages students to be unproductive due to its flexibility (5) it deprives students from determining areas for self-improvement since there is lack of guidance and feedback from teachers and instructors; (6) it does not facilitate practical application of theoretical knowledge; (7) it does not motivate the students to actively participate since there the teachers or instructors cannot monitor the students from their end. However, the students' Preference is Face-to-Face Classes as classes provide a more dynamic way of learning and it offers a lot more in terms of different learning methods to be utilized individually or as a whole class. The conduct of face-to-face classes requires medical students to be actively involved in the learning process.