Metacognition, the ability to self-regulate one's learning and performance, has been shown to improve student outcomes. Anatomy is recognized as one of the toughest courses in allied health curricula, and students could benefit from metacognitive activities. The purpose of this study was to explore the changes in metacognition of allied health students in an anatomy course and identify which groups need support with this skill. First-year physician assistant (MPAS), physical therapy (DPT), and occupational therapy (OTD) students (n = 129) were invited to participate. At the beginning and end of the course, students completed a questionnaire including the metacognitive awareness inventory (MAI) that assesses metacognition. Students were also asked to reflect on their examination performances using a modified Likert scale and participated in reflective discussion boards to encourage development of metacognitive skills, which were thematically analyzed. Paired metacognition scores had increased significantly by the end of the course. However, middle-performers anticipated high grades and were less satisfied with their grade, indicating a disconnect in their metacognition compared to high- and low-performers. Students' receptiveness to modifying study strategies to improve performance declined throughout the course; by mid-way through, they relied more on existing strategies. Increasing time constraints were frequently cited as a major factor when considering study strategies and modification of such strategies. To maximize the effectiveness of metacognitive activities, they should be positioned early in the course when students are most receptive. In addition, middle performers may benefit from additional support to improve metacognition.