Colleges and universities are beginning to invest in active learning (AL) classrooms in an effort to replace the traditional lecture style pedagogy that is frequently used by many professors in higher education (Eagan et al., 2014). This is a quantitative research study conducted at a medium-sized Midwestern university. Students were given the Community of Inquiry (CoI) Survey in three different classes. The research study compared students’ perceptions of Teaching Presence (TP), Social Presence (SP), and Cognitive Presence (CP) differences from classes first taught in a traditional auditorium lecture-style format, then taught in an AL classroom. This study shows that it is not the physical structure of AL classrooms that had an impact on students’ levels of TP, SP, and CP, but the instructional design of these classes that had an impact in these areas. The study also shows that when implementing AL classrooms, instructors need to make intentional design decisions to keep the levels of TP at high levels.