Despite the educational potential of Facebook and Moodle, there are still unanswered questions about their impact on the student learning experience in a well-defined instructional design framework. This study aimed to compare the learning experiences of students who used Moodle (control group) and Facebook (experimental group), in terms of Community of Inquiry presence indicators, i.e., cognitive, teaching, and social presence. Several learning activities for the development of learning environments were carried out by 97 students who were enrolled in instructional media design courses. Findings from quantitative and qualitative analysis indicated that students using either Moodle or Facebook as their learning platform had similar perceptions of teaching and cognitive presence; however, Facebook users had a better social presence in the Community of Inquiry than their Moodle counterparts. Another point worth noting is that the experimental group's female participants had better teaching presence, cognitive presence, and overall learning experience than their male peers.