The Covid-19 Movement Control Order imposed by the government converted the delivery of lessons to online learning in the education sector. Pharmaceutical chemistry is a core subject for pharmacy students and first-year students were taught the elucidation of the absolute configuration of active pharmaceutical ingredients (API). The objective of this study is to investigate the pharmacy students’ perceptions and performance on learning new knowledge related to the concept of absolute configuration on API through micro-learning. Students were introduced and assessed on the stereochemistry of new terminologies through micro-learning activities. Various 3D molecular model capture in video format was uploaded on YouTube(YT) and embedded in the Google Form(GF) online assessment. The students’ video navigation was captured with YT video analytics, students learning performance was through GF quiz assessment responses, and the student’s attitudes through questionnaire survey. In conclusion, the performance of student pharmacists in learning and applying new knowledge delivered through online distance micro-learning was comparable to face-to-face active learning. Both YT video analytics and GF responses allowed real-time monitoring and interventions. Nonetheless, students required more time to learn new knowledge online compared to face-to-face active learning. In conclusion, the designed virtual micro-learning enabled students to learn bite-sized new knowledge while training their spatial ability through the application of 3D molecular models with reinforcement through quizzes. The virtual micro-learning design is practical and economical without much technological investment or training for both the educator and learner with easy access in an open distance learning environment and post-Covid.