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This study investigated student perceptions of cognitive presence, self-regulation, and co-regulation as explained by three teaching presence sub-elements–instructional design, direct instruction, and facilitation–in an online case-based course. 113 online graduate students enrolled in an advanced instructional design course participated in the study. Data were collected through the Community of Inquiry survey and a shared metacognition questionnaire online survey. The findings revealed that students perceived Facilitation as a significant predictor of cognitive presence, and Direct Instruction as a significant predictor of both self-regulation and co-regulation. The findings highlight the importance of teaching presence for facilitating discourse to increase cognitive presence and direct instruction to increase self and co-regulation for maximizing the quality of online case-based instruction.